U.S. patent application number 17/166004 was filed with the patent office on 2021-07-15 for delta133p53beta and delta133p53gamma isoforms are biomarkers of cancer stem cells.
The applicant listed for this patent is Centre National de la Recherche Scientifique (CNRS), Universite de Montpellier. Invention is credited to Nikola Arsic, Philippe Fort, Gilles Gadea, Veronique Gire, Pierre Roux, Fanny Thomas.
Application Number | 20210214691 17/166004 |
Document ID | / |
Family ID | 1000005478062 |
Filed Date | 2021-07-15 |
United States Patent
Application |
20210214691 |
Kind Code |
A1 |
Roux; Pierre ; et
al. |
July 15, 2021 |
Delta133P53Beta and Delta133P53Gamma Isoforms Are Biomarkers of
Cancer Stem Cells
Abstract
The present invention is in the field of oncology, and more
particularly of cancer stem cells. It relates to a method for
producing cancer stem cells based on overexpression of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; a method for
predicting the risk that treatment with a chemotherapeutic
anti-cancer agent induces cancer stem cells in a subject suffering
from cancer from a cancer sample of said subject, based on
detection of an increase in .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms following chemotherapeutic
anti-cancer treatment; to therapeutic uses of a combination of
chemotherapeutic anti-cancer agent and an agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression;
and also to screening methods for anti-cancer stem cells
agents.
Inventors: |
Roux; Pierre; (Saint Gely-Du
Fesc, FR) ; Arsic; Nikola; (Montpellier, FR) ;
Gadea; Gilles; (Les Matelles, FR) ; Fort;
Philippe; (Castelnau-Le-Lez, FR) ; Thomas; Fanny;
(Montpellier, FR) ; Gire; Veronique; (Montpellier,
FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Centre National de la Recherche Scientifique (CNRS)
Universite de Montpellier |
Paris
Montpellier |
|
FR
FR |
|
|
Family ID: |
1000005478062 |
Appl. No.: |
17/166004 |
Filed: |
February 3, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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15547211 |
Jul 28, 2017 |
10920198 |
|
|
PCT/EP2016/052095 |
Feb 1, 2016 |
|
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17166004 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 2501/998 20130101;
G01N 2333/4748 20130101; C12Q 2600/118 20130101; C07K 14/4746
20130101; G01N 2500/10 20130101; C12Q 2600/106 20130101; C12N
5/0695 20130101; G01N 33/5011 20130101; C12Q 2600/156 20130101;
C12Q 1/6886 20130101; C12N 2510/00 20130101; A61K 31/704 20130101;
G01N 33/57484 20130101; C12N 2506/30 20130101; A61K 31/7048
20130101; G01N 33/5073 20130101; C12N 2503/00 20130101 |
International
Class: |
C12N 5/095 20060101
C12N005/095; G01N 33/574 20060101 G01N033/574; A61K 31/704 20060101
A61K031/704; A61K 31/7048 20060101 A61K031/7048; C07K 14/47
20060101 C07K014/47; C12Q 1/6886 20060101 C12Q001/6886; G01N 33/50
20060101 G01N033/50 |
Foreign Application Data
Date |
Code |
Application Number |
Jan 30, 2015 |
EP |
15305146.1 |
Claims
1-16. (canceled)
17. A method for predicting a risk of cancer metastasis in a
subject suffering from cancer from a cancer sample of said subject,
comprising: a) detecting sphere-forming cancer cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample; and b) concluding to the presence of a significant
risk of cancer metastasis in said subject if sphere-forming cancer
cells expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are detected and to the absence of a significant risk of
cancer metastasis in said subject if sphere-forming cancer cells
expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are not detected.
18. The method according to claim 17, wherein the subject is
suffering from one or more of: (i) solid cancers selected from the
group consisting of breast cancer, ovarian cancer, pancreatic
cancer, throat cancer, and gastrointestinal cancer including
colorectal cancer oesophageal cancer, gastric cancer, pancreatic
cancer, hepatocellular carcinoma, cholangiocellular cancer and
teratocarcinoma, or (ii) hematopoietic cancers selected from
leukaemias or lymphomas.
19. The method according to claim 18, wherein the subject is
suffering from breast cancer or colorectal cancer.
20. The method according to claim 17, wherein the cancer sample
from which the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is measured in step a) is selected
from: (i) a cancer biopsy or a complete or partial cancer surgical
resection, or (ii) a blood sample.
21. The method according to claim 17, wherein sphere-forming cancer
cells expressing .DELTA.133p53.beta. isoform or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample are detected in step a).
22. The method according to claim 17, wherein sphere-forming cancer
cells in step a) are detected by performing an assay comprising the
steps of: (i) resuspending cancer cells into a serum-free medium
and plating them into tissue culture dishes, to which mammalian
cells poorly adhere, at a seeding density between 250 and 2500
cells/cm.sup.2; (ii) incubating the cancer cells during 7 to 15
days; and (iii) counting spheres that are at least 50 .mu.m
large.
23. The method according to claim 22, wherein the resuspending of
cancer cells in step (i) is performed in the presence of specific
growth factors EGF and bFGF; the incubating of step (ii) is
performed at 37.degree. C. under 5% CO.sub.2 atmosphere, and the
counting in step (iii) is performed by a phase-contrast
microscope.
24. The method according to claim 17, wherein in step a)
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms are detected
at nucleic acid level by measuring the amount of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms mRNA or
corresponding cDNA or at protein level.
25. The method according to claim 24, wherein in step a)
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms are detected
q-RT-PCR.
26. The method according to claim 17, wherein said method further
comprises after step b), a step c) of treating the subject
determined as being at a significant risk of cancer metastasis by
administering to the said subject agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
expression.
27. The method according to claim 26, wherein the agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression is
antisense RNA or interfering RNA (iRNA).
28. The method according to claim 27, wherein the agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression is
selected from small interfering RNAs (siRNAs) or short hairpin RNAS
(shRNAs).
29. The method according to claim 17, wherein said method further
comprises after step b), a step c) of treating the subject, wherein
(i) if the subject is determined as being at a significant risk of
cancer metastasis, an agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression and an anticancer
treatment is administered to the subject, or (ii) if the subject is
determined as not being at a significant risk of cancer metastasis,
an anticancer treatment is administered to the subject.
30. The method according to claim 29, wherein the agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression is
antisense RNA or interfering RNA (iRNA).
31. The method according to claim 30, wherein the agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression is
selected from small interfering RNAs (siRNAs) or short hairpin RNAS
(shRNAs).
32. The method according to claim 29, wherein the anticancer
treatment is performed by a chemotherapeutic anti-cancer agent.
33. The method according to claim 32, wherein the chemotherapeutic
anti-cancer agent is selected from topoisomerase II inhibitors,
anti-tubuline agents, and antimetabolites.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 15/547,211, filed Jul. 28, 2017, which is a National Stage
Application under 35 U.S.C. 371 of co-pending PCT application
PCT/EP2016/052095 designating the United States and filed Feb. 1,
2016; which claims the benefit of EP application number 15305146.1
and filed Jan. 30, 2015 each of which are hereby incorporated by
reference in their entireties.
TECHNICAL FIELD OF THE INVENTION
[0002] The present invention is in the field of oncology, and more
particularly of cancer stem cells. It relates to a method for
producing cancer stem cells based on overexpression of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; a method for
predicting the risk that treatment with a chemotherapeutic
anti-cancer agent induces cancer stem cells in a subject suffering
from cancer from a cancer sample of said subject, based on
detection of an increase in .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms following chemotherapeutic
anti-cancer treatment; to therapeutic uses of a combination of
chemotherapeutic anti-cancer agent and an agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression;
and also to screening methods for anti-cancer stem cells
agents.
BACKGROUND ART
[0003] Cancer stem cells (CSCs) are cancer cells with the ability
to perpetuate through self-renewal and the ability to generate all
distinct cell types found in their original tumor. CSCs usually
represent a small fraction of the cells within a malignant tumor.
However, owing to their capacity for self-renewal and asymmetric
division, CSCs are believed to be the source of unlimited tumor
regeneration, heterogeneity and resistance to standard
treatment.
[0004] As CSC eradication seems necessary for the final cure of
many cancer types in humans, it is vital to better understand their
biology. However, due to their low abundance in cancer tissues,
their study is difficult. There is thus a need for methods to
generate sufficient numbers of CSCs for further study.
[0005] The tumor suppressor p53 exercises its functions mainly
through modulation of gene expression and it was proposed to be the
"guardian of the genome" (Lane, 1992). However, p53 functions are
ubiquitously altered in cancer cells by mutations/perturbation of
its signaling pathways and loss of p53 activity is a prerequisite
for cancer development. Mutant p53 is thought to play a pivotal
role in promoting invasion, favoring cancer cell exit from the
primary tumor site and dissemination, ultimately leading to
metastasis formation (Gadea et al., 2007a, b; Muller et al., 2009;
Roger et al., 2010; Vinot et al., 2008).
[0006] Recent reports have documented the role of p53 in stem cell
homeostasis and pluripotency. Wild type (wt) p53 counteracts
somatic cell reprogramming (Hong et al., 2009; Kawamura et al.,
2009; Liu et al., 2009; Utikal et al., 2009), whereas mutant p53
stimulates induced pluripotent stem (iPS) cell formation (Sarig et
al., 2010). A recent genome-wide study demonstrated that p53
regulates approximately 3600 genes in mouse ES cells (Li et al.,
2012). The group of positively regulated genes (about 2000) is
enriched in genes responsible for cell differentiation, while the
negatively regulated group (about 1600 genes) is involved mainly in
maintaining the ES cell status. p53 represses key regulators of the
stem cell phenotype, such as Oct 3/4, Nanog, Sox 2 and c-Myc
(Yamanaka factors, Li et al., 2012). Stress-induced activation of
the p53 signaling pathway in ES cells leads to cell differentiation
rather than apoptosis and cell death (Zhao and Xu, 2010).
Accordingly, p53 hinders cell reprogramming through the p21
signaling pathway (Hong et al., 2009). Depletion of p53
significantly increases cell reprogramming efficacy and facilitates
iPS cell generation using only two factors from the Yamanaka
cocktail (SOX 2 and OCT 3/4) (Kawamura et al., 2009). Consequently,
p53 might be considered not only as the guardian of the genome, but
also as the guardian of reprogramming.
[0007] All these functions are associated with full-length p53
(i.e., the TAp53.alpha. isoform). However, the TP53 gene encodes at
least twelve different physiological isoforms [TAp53 (.alpha.,
.beta. and .gamma.), .DELTA.40p53 (.alpha., .beta. and .gamma.),
.DELTA.133p53 (.alpha., .beta. and .gamma.) and .DELTA.160p53
(.alpha., .beta. and .gamma.)] (Bourdon, 2007) via several
mechanisms: use of alternative promoters (the TA and .DELTA.133
isoforms), alternative intron splicing (intron 2: .DELTA.40
isoforms and intron 9: .alpha., .beta. and .gamma. isoforms) and
alternative translational initiation sites (.DELTA.40 isoforms and
.DELTA.160 isoforms). A scheme summarizing the features of isoforms
.alpha., .beta. and .gamma. of TAp53, .DELTA.40 p53, and
.DELTA.133p53 is presented in FIG. 1A. The TAp53a isoform is the
best described and classically mentioned in the literature as p53.
Basically, p53 isoforms can be divided in two groups: long isoforms
that contain the transactivation domain (TA and .DELTA.40) and
short isoforms without transactivation domain (.DELTA.133 and
.DELTA.160). Furthermore, the .beta. and .gamma. isoforms do not
contain the canonical C-terminal oligomerization domain, but an
additional domain with unknown function(s) to date (Khoury and
Bourdon, 2011). Several clinical studies have reported that p53
isoforms are abnormally expressed in many human cancer types
(Avery-Kiejda et al., 2014; Boldrup et al., 2007; Bourdon et al.,
2005; Bourdon et al., 2011; Hofstetter et al., 2012). As
differential expression of p53 isoforms can affect p53 tumor
suppressor activity, their deregulated expression could contribute
to tumorigenesis in cancers that express wild type p53. For
instance, the N-terminal truncated isoforms .DELTA.40p53 and
.DELTA.133p53 exert dominant negative functions towards wild type
p53, by inhibiting transactivation of its target genes and by
interfering with p53-dependent growth suppression (Bourdon et al.,
2005; Davidson et al.; Fujita et al., 2009). Moreover, .DELTA.40p53
can modulate transcription by reorienting p53 signaling (Hafsi et
al., 2013; Takahashi et al., 2014). All these results on the
interactions between p53 and its N-terminal isoforms suggest that,
in specific conditions, these isoforms may either enhance or
decrease the basal level of p53 activity, thus contributing to set
a threshold for p53-dependent responses to endogenous or exogenous
stimuli.
[0008] WO2009/029054 suggests to treat or prevent cancer by
reducing or inhibiting expression of at least one p53 isoform
modulating expression or activity of p53, in particular by reducing
or inhibiting expression of N-terminal truncated .DELTA.113p53 or
.DELTA.133p53 isoforms, which are considered to act as dominant
negative regulators of full-length p53. While both .DELTA.113p53
and .DELTA.133p53 isoforms are mentioned, data is provided only for
.DELTA.113p53. In addition, among the three .DELTA.133 isoforms of
p53, WO2009/029054 only suggests the use of .DELTA.133p53 (which is
also referred to as .DELTA.133p53.alpha.), but not of isoforms
.DELTA.133p53.beta. and .DELTA.133p53.gamma..
[0009] WO2011/000891 describes that expression of isoforms
.DELTA.133p53.beta. in cancer cells is a marker of increased risk
of cancer metastasis. On this basis, this application proposes
measuring the aggressiveness of cancer in a subject and determining
the subject's response to an anti-cancer therapy based on
determination of the expression level of .DELTA.133p53.alpha. (also
referred to as .DELTA.133p53), .DELTA.133p53.beta. or
.DELTA.133p53.gamma. in a cancer sample of said subject. The method
of determining the subject's response to an anti-cancer therapy is
based on the fact that metastatic cancer patients often do not
respond positively to conventional anticancer therapy.
WO2011/000891 further proposes screening potential anti-metastatic
compounds based on the ability of test compounds to decrease the
expression level of .DELTA.133p53.alpha. (also referred to as
.DELTA.133p53), .DELTA.133p53.beta. or .DELTA.133p53.gamma. in a
cell expressing .DELTA.133p53.alpha. (also referred to as
.DELTA.133p53), .DELTA.133p53.beta. or .DELTA.133p53.gamma.. In
light of WO2011/000891, it clearly appears that detecting the
expression of at least one of .DELTA.133p53.alpha.,
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoforms is indicative
for risk of metastatic cancer. Furthermore, it suggests that these
isoforms may be involved in cell invasiveness by enhancing cell
motility. However, this document does not suggest that said cell
invasiveness is linked to the production of cancer stem cells.
[0010] In this respect, it should be made clear that while
invasiveness is necessary for metastasis, it is not synonymous of
the production of cancer stem cells. In particular, while both
invasiveness and cancer stem cells are associated to metastasis,
this does not mean that these two notions are equivalent.
[0011] This is illustrated by the fact that some genes, which are
known to be associated to invasiveness, are not able to generate
cancer stem cells, in particular alone, without the previous or
concomitant induction of overexpression of transcription factors
known to be useful of reprogramming cells towards pluripotency,
such as Sox 2, Oct 3/4 and Nanog.
[0012] For instance, as explained above, WO2011/000891 suggests
that .DELTA.133p53.alpha., .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoforms may be involved in cell invasiveness
by enhancing cell motility. Similarly, Bernard et al-2013 also
suggests that specifically the .DELTA.133p53.alpha. and
.DELTA.133p53.gamma. isoforms, but not .DELTA.133p53.beta.,
stimulate angiogenesis and are thus involved in invasiveness.
However, WO2012/044979 suggests that .DELTA.133p53 (also referred
to as .DELTA.133p53.alpha.) may be used to produce cancer stem
cells only when co-expressed with another reprogramming factor,
such as OCT4, SOX2 or c-myc. In addition, the inventors found that
.DELTA.133p53.alpha. is actually not able, in the absence of
another reprogramming factor, such as OCT4, SOX2 or c-myc, to
generate cancer stem cells.
[0013] It should be noted that it was generally considered in the
prior art that overexpression of transcription factors known to be
useful of reprogramming cells towards pluripotency, such as Sox 2,
Oct 3/4 and Nanog is considered as a prerequisite for reprogramming
cells, including cancer cells, towards pluripotency.
[0014] Therefore, while many genes have been disclosed in the prior
art as involved in invasiveness and metastasis, this does not help
skilled persons to identify genes that would be able, without the
previous or concomitant induction of overexpression of
transcription factors known to be useful of reprogramming cells
towards pluripotency, such as Sox 2, Oct 3/4 and Nanog, to
reprogram cancer cells towards pluripotency and thus to generate
cancer stem cells.
SUMMARY OF THE INVENTION
[0015] In the context of the present invention, the inventors have
now found that .DELTA.133p53.beta. isoform (and also
.DELTA.133p53.gamma. to a lesser extent), but not
.DELTA.133p53.alpha. isoform (also referred to as .DELTA.133p53
isoform), is not only a marker of a risk of cancer metastasis, but
actually promotes cancer stem cell phenotype. In particular,
expression of .DELTA.133p53.beta. isoform (and also
.DELTA.133p53.gamma. to a lesser extent), but not of
.DELTA.133p53.alpha. isoform (also referred to as .DELTA.133p53
isoform), promotes cancer cell sphere-forming activity, and also
promotes Sox 2, Oct 3/4 and Nanog expression (but not c-Myc),
transcription factors known to be useful of reprogramming cells
towards pluripotency.
[0016] This finding was not expected, since not all markers of
metastasis risk are involved in development of cancer stem cells.
For example, WO2011/000891 suggests detecting the presence of
.DELTA.133p53.alpha. isoform in order to determine if the tested
patient risk to develop metastatic cancer. Other authors (Bernard
et al., 2013) have also suggested that .DELTA.133p53.alpha. isoform
is able to stimulate angiogenesis and is thus involved in cancer
cell invasiveness. However, in the present invention, the inventors
demonstrated that .DELTA.133p53.alpha. isoform is unable to induce
the development of cancer stem cells. Indeed, while increasing
evidences suggest that CSCs and metastasis development are closely
linked, many questions are still unsolved concerning the precise
role of CSCs in metastasis development.
[0017] The above finding the inventors is very important since it
provides a mean for producing high numbers of CSCs, thus permitting
to study and better understand their biology, a crucial point for
improving anticancer therapies.
[0018] In a first aspect, the present invention thus relates to a
method for producing cancer stem cells, comprising: [0019] a)
transducing cancer cells with a vector expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; [0020] b)
culturing transduced cancer cells in a medium supporting expansion
of transduced cancer cells; and [0021] c) isolating cancer stem
cells.
[0022] The inventors further surprisingly found that anticancer
treatment of cancer cells by etoposide (a topoisomerase II
inhibitor) may not be only inefficient but may further promote
cancer sternness by increasing .DELTA.133p53.beta. expression
level, which itself increases the expression level of transcription
factors specifically expressed by stem cells, such as Oct 3/4,
Nanog and Sox 2. As a result, treating cancer patients with
etoposide may promote CSC formation and would then be rather
deleterious than useful.
[0023] The present invention thus also relates to a method for
predicting the risk that treatment with a chemotherapeutic
anti-cancer agent induces cancer stem cells in a subject suffering
from cancer from a cancer sample of said subject, comprising:
[0024] a) measuring in vitro the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample, untreated with the chemotherapeutic anti-cancer
agent; [0025] b) treating said cancer sample with said
chemotherapeutic anti-cancer agent; [0026] c) measuring in vitro
the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in the treated cancer sample; [0027]
d) comparing the values obtained in steps a) and c); and [0028] e)
concluding to: [0029] (i) the presence of a significant risk that
treatment with said chemotherapeutic anti-cancer agent induces
cancer stem cells in said subject if the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms measured in
step c) is higher than the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms measured in step a), or [0030]
(ii) the absence of a significant risk that treatment with said
chemotherapeutic anti-cancer agent induces cancer stem cells in
said subject if the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms measured in step c) is lower than
or equal to the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms measured in step a).
[0031] Based on the same finding of the inventors that anticancer
treatment of cancer cells by etoposide (a topoisomerase II
inhibitor) may not be only inefficient (resistance to treatment)
but may further promote cancer sternness by increasing
.DELTA.133p53.beta. expression level, the present invention also
relates to a chemotherapeutic anti-cancer agent, for use in the
treatment of cancer in a subject suffering from a cancer, wherein
said chemotherapeutic anti-cancer agent is administered to said
subject in combination with an agent reducing .DELTA.133p53.beta.
or .DELTA.133p53.gamma. isoform expression.
[0032] Similarly, the present invention also relates to a method
for treating cancer in a subject suffering from a cancer,
comprising: [0033] a) Administering to said subject a
therapeutically efficient amount of an agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression;
and [0034] b) Administering to said subject a therapeutically
efficient amount of a chemotherapeutic anti-cancer treatment.
[0035] The results obtained by the inventors show that
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform expression
promotes cancer stem cell potential, in particular by upregulating
expression of transcription factors Sox 2, Oct 3/4 and Nanog,
suggesting that expression of .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform may be an early event of reprogramming
of cancer cells towards cancer stem cells, and that detection of
other cancer stem cells features in addition to detection of
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform expression may
improve the reliability of prediction of a risk of cancer
metastasis in a subject suffering from cancer. The present
invention thus also relates to a method for predicting a risk of
cancer metastasis in a subject suffering from cancer from a cancer
sample of said subject, comprising:
a) detecting sphere-forming cancer cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample; and b) concluding to the presence of a significant
risk of cancer metastasis in said subject if sphere-forming cancer
cells expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are detected and to the absence of a significant risk of
cancer metastasis in said subject if sphere-forming cancer cells
expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are not detected. .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform expression promoting cancer stem cell
potential may also be used to predict a risk of cancer relapse in a
treated cancer subject after successful elimination of most cancer
cells.
[0036] The present invention thus also relates to a method for
predicting a risk of cancer relapse in a treated cancer subject
from a cell sample of said subject, comprising:
a) detecting the expression of .DELTA.133p53.beta. isoform, of
.DELTA.133p53.gamma. isoform, or of both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms; and b) concluding to the presence of
a significant risk of cancer relapse in said subject if the
expression of .DELTA.133p53.beta. isoform, of .DELTA.133p53.gamma.
isoform, or of both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms is detected and to the absence of a significant risk of
cancer relapse in said subject if neither the expression of
.DELTA.133p53.beta. isoform nor the expression of
.DELTA.133p53.gamma. isoform are detected.
[0037] Based on the same finding that .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform expression promotes cancer stem cell
potential, in particular by upregulating expression of
transcription factors Sox 2, Oct 3/4 and Nanog, suggesting that
expression of .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
may be an early event of reprogramming of cancer cells towards
cancer stem cells, the present invention also relates to a method
for screening potential anti-cancer stem cells compounds,
comprising:
a) providing sphere-forming cancer stem cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; b)
contacting said cancer stem cells with a test compound; c)
measuring in vitro the expression level of said .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms in treated cells and/or the
sphere-forming ability of treated cells; d) selecting said test
compound as a potential anti-cancer stem cells compound if the
expression level of said .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in treated cells is lower than before
treatment with the test compound, and/or if the sphere-forming
ability of treated cells is lower than before treatment with the
test compound.
DESCRIPTION OF THE FIGURES
[0038] FIGS. 1A-1G. Selective depletion of p53 isoforms affects the
sphere-forming ability of MCF-7 cells. A. Schematic representation
of p53 isoforms with the targets of the different shRNAs (Sh) used
in this study. The calculated molecular weights of the different
isoforms are indicated. TA: transactivation domain; 5'UTR: 5'
untranslated region; DBD: DNA binding domain; NLS: nuclear
localization sequence; OD: oligomerization domain. B. Mammosphere
quantification in MCF-7 cells after transduction of Sh1, Sh2, Sh3
Sh4 and Sh5 (n=3). C, D and E. Western blot analysis of p53 isoform
depletion in the corresponding cells. F. and G. RT-qPCR
quantification of the expression level of c-Myc, Sox 2, Oct 3/4 and
Nanog (F) as well as of .DELTA.133p53 (.alpha., .beta. and .gamma.)
and p53 .beta. isoforms (p53 TAB, .DELTA.40p53.beta.,
.DELTA.133p53.beta., and .DELTA.160p53.beta.) (G) after
transduction with Sh1 and Sh2 (n=4).
[0039] FIGS. 2A-2D. Analysis of key pluripotency/reprogramming
genes expression following changes in p53 isoform levels. A.
Western blot analysis of the expression of key
pluripotency/reprogramming factors (c-Myc, Nanog, Sox 2 and Oct
3/4) after p53 isoform depletion using Sh1, Sh2, Sh3 or/and Sh4 and
in control cells. B and C. Mammosphere quantification in MCF-7
cells upon p53 knock-down with Sh6 (n=3) (B) and western blot
analysis of p53 depletion in the corresponding cells (C) and (D)
Colospheres formation in SW480 colon carcinoma cells wherein
.DELTA.133p53 isoforms were knocked down using Sh3.
[0040] FIGS. 3A-3G. .DELTA.133p53B promotes cancer stem cell
potential in MCF-7 cells. A and B. Mammosphere quantification in
MCF-7 cells after silencing with Sh2 (shRNAs against the TA and
.DELTA.40 isoforms) or with Sh2 and Sh6 (against the 3' end of the
.alpha. isoforms) (A) and western blot analysis to confirm p53
depletion in the corresponding cell cultures (B) (n=3). C.
Representative FACS dot blots for the double labeling of CD24 and
CD44 in MCF-7 transduced with Sh Luc (Control), Sh2 or Sh2+6. D and
E. Mammosphere quantification in MCF-7 cells after
.DELTA.133p53.beta. or .gamma. overexpression (D) and RT-qPCR
analysis of c-Myc, Sox 2, Oct 3/4 and Nanog (E) expression in the
corresponding cells (n=4). F. Mammosphere quantification in MCF-7
cells that overexpress .DELTA.133p53.beta. after harvesting and
re-plating of the primary mammospheres. G. Mammosphere
quantification in MCF-7 cells in which all p53 isoforms have been
silenced with Sh1 and after expression in the same cells of
Sh1-resistant .DELTA.133p53.beta. (n=3).
[0041] FIG. 4. Western blot analysis of p53 isoforms transduced in
MCF-7 cells (Sapu antibody).
[0042] FIGS. 5A-5G. Derivation and characterization of the C3LND
cell line. A. Schematic representation of the approach used to
derive the highly metastatic C3LND sub-clone starting from the
MDA-MB231 D3H2LN cell line. B. Major oncogenic characteristics of
the sub-clones obtained during C3LND isolation starting from
MDA-MB-231 D3H2LN cells. LN: Lymph nodes; Ax/Br:
Axillary/Branchial. C. Quantification of primary tumor growth (n=5
for each group and time point). D. Quantification of
bioluminescence during tumor growth (n=5 for each group and time
point). E. RT-qPCR analysis of c-Myc, Oct 3/4, Nanog and Sox 2
expression in C3LND cells after overexpression of the
.DELTA.133p53.beta. isoform (n=3). F. Western blot analysis of p53
isoform transduced with Sh3 in MDA-MB-231 C3LND. G. Quantification
of luminescence (n=2 for each group and time point).
[0043] FIGS. 6A-6K. Evaluation of the cancer stem cell features of
the MDA-MB 231 D3H2LN and C3LND cell lines. A. Mammosphere
quantification in the modestly metastatic, parental MDA-MB-231
D3H2LN and the derived, highly metastatic C3LND cell line (n=3). B.
RT-qPCR analysis of .DELTA.133p53 (.alpha., .beta. and .gamma.)
isoforms expression in MDA-MB-231 D3H2LN and C3LND cells (n=4). C.
RT-qPCR quantification of c-Myc, Oct 3/4, Nanog and Sox 2
expression in MDA-MB-231 D3H2LN and C3LND cells (n=4). D. Western
blot analysis of .DELTA.133p53.beta.-Flag transduced in MDA-MB 231
D3H2LN cells (Flag antibody). E. RT-qPCR analysis of c-Myc, Oct
3/4, Nanog and Sox 2 expression in MDA-MB-231 D3H2LN cells after
.DELTA.133p53.beta. overexpression (n=4). F. Mammosphere
quantification in MDA-MB-231 D3H2LN cells that overexpress
.DELTA.133p53.beta.. G. Mammosphere quantification in MDA-MB-231
C3LND transduced with Sh3 (n=3). H. RT-qPCR analysis of
.DELTA.133p53 (.alpha., .beta. and .gamma.) isoforms expression in
MDA-MB-231 C3LND transduced with Sh3. I. RT-qPCR quantification of
c-Myc, Oct 3/4, Nanog and Sox 2 expression in MDA-MB-231 C3LND
cells transduced with Sh3 (n=4). J. Representative FACS dot plots
for the double labeling of CD44 and CD24 in MDA-MB-231 C3LND
transduced with Sh Luc (Control), or Sh3. K. Quantification of
distant metastasis in brain and femur using bioluminescence imaging
(n=7/5) 25 days after the implantation.
[0044] FIGS. 7A-7I. Chemotherapy treatment of MCF-7 breast cancer
cells up-regulates .DELTA.133p53 isoform expression and activates
key pluripotency genes. A. Western blot analysis of p53, p21 and
c-Myc expression in MCF-7 cells after treatment with increasing
doses of etoposide for 16 hours (D01 antibody). B. RT-qPCR analysis
of c-Myc expression in MCF-7 cells upon treatment with increasing
doses of etoposide (n=4). C. RT-qPCR analysis of .DELTA.133p53
(.alpha., .beta. and .gamma.) isoforms expression in MCF-7 cells
after etoposide treatment (n=4). D. Western blot analysis of p53
isoform expression in MCF-7 cells after etoposide treatment. (Sapu
antibody). E. RT-qPCR analysis of Sox 2, Oct 3/4 and Nanog
expression in MCF-7 cells upon treatment with increasing doses of
etoposide (n=4). F. RT-qPCR analysis of .DELTA.133p53 (.alpha.,
.beta. and .gamma.), Sox 2, Oct 3/4 and Nanog expression in control
and MCF-7 cells transduced with Sh3 upon etoposide treatment (n=4).
G. Mammosphere quantification in MCF-7 cells transduced with Sh2
and treated with 50 ng/ml/day etoposide for 7 days (n=3). H and I.
RT-qPCR analysis of c-Myc, Nanog, Oct 3/4 and Sox 2 (H) and
6.133p53 (.alpha., .beta. and .gamma.) isoforms (I) expression in
MCF-7 cells transduced with Sh2 and treated with 50 ng/ml/day
etoposide for 7 days (n=4).
[0045] FIGS. 8A-8D. Etoposide treatment of MDA-MB-231 D3H2LN cells
up-regulates .DELTA.133p53 isoform expression and activates key
pluripotency genes. A. Western blot analysis of p53, p21 and c-Myc
expression in MDA-MB-231 D3H2LN cells after treatment with
increasing doses of etoposide for 16 hours. B. RT-qPCR analysis of
c-Myc expression in MDA-MB-231 D3H2LN cells upon treatment with
increasing doses of etoposide (n=4). C. RT-qPCR analysis of
.DELTA.133p53 (.alpha., .beta. and .gamma.) isoforms expression in
MDA-MB-231 D3H2LN cells after etoposide treatment (n=4). D. RT-qPCR
analysis of Nanog, Oct 3/4 and Sox 2 expression in MDA-MB-231
D3H2LN cells upon treatment with increasing doses of etoposide
(n=4).
DETAILED DESCRIPTION OF THE INVENTION
Definitions
P53 Isoforms
[0046] P53 isoforms are presented in FIG. 1A.
[0047] In addition, Table 1 below provides amino acids and nucleic
acid sequences of full-length p53 (denoted as "p53"), and of
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms.
TABLE-US-00001 TABLE 1 Amino acids and nucleic acid sequences of
full-length p53 (denoted as "p53"), and of .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms. Amino acids sequence Nucleic acid
sequence (SEQ ID NO:/Genbank (SEQ ID NO:/Genbank Isoform accession
number) accession number) .DELTA.133p53.beta. SEQ ID NO:1 / SEQ ID
NO:2 / NP_001119588.1 NM_001126116.1 .DELTA.133p53.gamma. SEQ ID
NO:3 / SEQ ID NO:4 / NP_001119589.1 NM_001126117.1 p53 SEQ ID NO:5
/ SEQ ID NO:6 / NP_000537.3 NM_000546.4
Cancer, Cancer Stem Cells, Chemotherapeutic Anti-Cancer Treatments,
Anti-Cancer Stem Cells Agents
[0048] In the present description, "cancer" refers to a malignant
neoplasm characterized by deregulated or uncontrolled cell growth.
In particular, a "cancer cell" refers to a cell with deregulated or
uncontrolled cell growth.
[0049] The term "cancer" includes primary malignant tumours (e. g.,
those whose cells have not migrated to sites in the subject's body
other than the site of the original tumor) and secondary malignant
tumours (e. g., those arising from metastasis, the migration of
tumour cells to secondary sites that are different from the site of
the original tumour). Such cancer may notably be selected from the
group of solid cancers, and in particular from the group consisting
of breast cancer, colorectal cancer ovarian cancer, digestive
cancers (also referred as gastrointestinal cancer including
colorectal cancer, oesophageal cancer, gastric cancer, pancreatic
cancer, hepatocellular carcinoma, cholangiocellular cancer and
teratocarcinoma), pancreatic cancer and throat cancer, particularly
of human subject, the more preferred is breast cancer, a colorectal
cancer gastrointestinal cancer, lung cancer and prostate cancer,
and even more preferably a breast cancer or a colorectal cancer.
Such cancer may also be selected from the group of hematopoietic
cancers, and in particular from the group consisting of leukaemias
and lymphomas, particularly of human subject.
[0050] In the present description, "cancer relapse" refers to the
return of the cancer or the signs and symptoms thereof after a
period of improvement.
[0051] By "cancer sample", it is meant any sample comprising cancer
cells, including but not limited to a cancer biopsy or a complete
or partial cancer surgical resection, or a blood sample. Indeed, it
is well known in the art that circulating cancer cells are present
in blood.
[0052] By "untreated cancer sample" is meant a cancer sample that
has not been treated with a chemotherapeutic anti-cancer agent. In
contrast, by "treated cancer sample" is meant a cancer sample that
has been treated with a chemotherapeutic anti-cancer agent.
[0053] By "non-cancerous cell sample" it is meant any sample
comprising or supposed to comprise a healthy non cancer cells
including but not limited to tissue biopsy or blood sample.
[0054] In the present description, a "chemotherapeutic anti-cancer
agent" refers to any chemical drug used for anticancer therapy.
Chemotherapeutic anti-cancer agent may be any one of those listed
by the American Cancer Society. Such chemotherapeutic anti-cancer
agent notably includes any of the following conventional
anti-cancer treatments: topoisomerase II inhibitors (including
etoposide, tenoposide, doxorubicine, daunorubicin, mitoxantrone,
and amsacrine), anti-tubuline agent (including taxanes such as
paclitaxel and docetaxel; and vinca alkaloids such as vinblastine,
vincristine, vindesine, and vinorelbine), antimetabolites (such as
pyrimidine analogue 5-Fluorouracil (5-FU).
[0055] In the present description, a "cancer stem cells"
(abbreviated as "CSCs") refers to cancer cells with features
associated to normal stem cells, such as the ability to give rise
to all cell types found in a particular cancer sample. CSCs are
also characterized by the expression of transcription factors
specifically expressed in stem cells, such as Oct 3/4, Nanog and
Sox 2; the ability to form spheres in appropriate conditions; the
presence of side populations (SP); and/or the expression or
non-expression of surface markers associated to cancer stem cells.
Based on the teachings of Tirino et al., 2013, surface phenotype,
detection of side-population (SP) phenotypes by Hoechst 33342
exclusion, of sphere-forming ability, and/or detection of aldehyde
dehydrogenase (ALDH) activity of various cancer stem cells are
disclosed in Table 2a below.
TABLE-US-00002 TABLE 2a surface phenotype, detection of
side-population (SP) phenotypes by Hoechst 33342 exclusion, of
sphere-forming ability, and/or detection of aldehyde dehydrogenase
(ALDH) activity of various cancer stem cells as disclosed in Tirino
et al., 2013. HNSCC: head and neck squamous cell carcinoma.
Detection Sphere- CSC surface of SP forming ALDH Tumor type
phenotype phenotypes ability activity Breast cancer
CD44.sup.+CD24.sup.-/low / Yes / Glioblastoma CD133.sup.+ / Yes /
Melanoma CD20.sup.+ / Yes / Prostate cancer
CD44.sup.+/.alpha..sub.2.beta..sub.1.sup.hi/CD133.sup.+ / Yes /
Ovarian cancer / Yes Yes / Gastric cancer CD44.sup.+ Yes / / Lung
cancer CD133.sup.+ Yes Yes / HNSCC CD44.sup.+ / / / Osteosarcoma
CD133.sup.+, CD117.sup.+, Stro-1.sup.+ Yes Yes Yes Chondrosarcoma
CD133.sup.+ Yes Yes / Synovial sarcoma CD133.sup.+ / / / Ewing's
sarcoma CD133.sup.+ / / Yes Rhabdomyosarcoma CD133.sup.+ / / /
Mesenchymal / Yes / / neoplasms
[0056] Table 2b below shows cell surface phenotype of CSC
identified in hematological malignancies:
TABLE-US-00003 TABLE 2b surface phenotype detection summarized by
Schatton et al. (2009). Tumor type Cell surface markers AML (acute
myeloid leukemia) CD34.sup.+CD38.sup.- CD34.sup.+CD38.sup.-
CD34.sup.+CD38.sup.- B-ALL (acute lymphoblastic leukemia)
CD34.sup.+CD10.sup.-/CD34.sup.+CD19.sup.-
CD34.sup.+CD38.sup.-CD19.sup.+ Multiple Myeloma
CD34.sup.-CD138.sup.- T-ALL (acute lymphoblastic leukemia)
CD34.sup.+CD4.sup.-/CD34.sup.+CD7.sup.-
[0057] In order to experimentally check the "sternness" of a given
cancer cell population, often rely on xenotransplantation assays in
immunocompromised mice using human tumor biopsy-derived cancer
subpopulations sorted for the presence or absence of a particular
candidate CSC marker or set of markers as indicated above (Schatton
et al., 2009). Cancer stem cell may by also defined by
xenotransplantation in zebrafish (Dovey et al., 2009).
[0058] Traditionally, CSCs have also been identified through sphere
formation in cell culture with matrigel or extra-low attachment
conditions (Le Cheng et al, 2009).
[0059] In the present description, "sphere", "spheroid" or
"tumorsphere" refers to a solid, spherical formation developed from
the proliferation of one cancer cell. Such spheres are easily
distinguishable from single or aggregated cells as the cells appear
to become fused together and individual cells cannot be identified.
Their size may vary between 50 and 250 .mu.m. The ability to form
spheres is considered to be associated to the presence of cancer
stem cells. Such spheres as defined in the present invention are
distinct from commonly known blebbes, as defined for example by
Charras (2008). In particular, blebs are protrusions of the cell
membrane of one cell which are the result of actomyosin contraction
of the cortex causing either transient detachement of the cell
membrane from the actin cortex or a rupture in the actin cortex. In
contrast, the spheres are formed by the aggregation of several
cells.
[0060] In addition to the surface markers defined in Tables 2a and
2b above for CSCs of various origin, CSCs generally also express
surface markers of normal stem cells, such as the carbohydrate
epitopes TRA-1-60 and TRA-1-81 recognized by commercially available
anti-TRA-1-60 and anti-TRA-1-81 monoclonal antibodies.
[0061] As used herein, a "therapeutically efficient amount" refers
to an amount sufficient for the intended use. For a
chemotherapeutic anti-cancer agent, it refers to an amount
sufficient to reduce cancer growth or spreading. For an agent
reducing .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
expression, it refers to an amount sufficient to significantly
reduce .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
expression level.
Vectors
[0062] A "plasmid vector" as used herein refers to a replicable DNA
construct.
[0063] The term "viral vector" as used herein refers to a nucleic
acid vector that includes at least one element of a virus genome
and may be packaged into a viral particle. The terms "virus",
"virions", "viral particles" and "viral vector particle" are used
interchangeably to refer to viral particles that are formed when
the nucleic acid vector is transduced into an appropriate cell or
cell line according to suitable conditions allowing the generation
of viral particles. In the context of the present invention, the
term "viral vector" has to be understood broadly as including
nucleic acid vector (e.g. DNA viral vector) as well as viral
particles generated thereof. The term "infectious" refers to the
ability of a viral vector to infect and enter into a host cell or
subject.
[0064] As used herein, the term "regulatory elements" or
"regulatory sequence" refers to any element that allows,
contributes or modulates the expression of nucleic acid molecule(s)
in a given host cell or subject, including replication,
duplication, transcription, splicing, translation, stability and/or
transport of the nucleic acid(s) or its derivative (i.e. mRNA).
Other Definitions
[0065] In the present description, the term "subject" refers to
mammals, e. g., humans, dogs, cows, horses, kangaroos, pigs, sheep,
goats, cats, mice, rabbits, rats, and transgenic non-human animals.
In preferred embodiments of the present invention, a subject is a
human subject, and more preferably a woman in the context of breast
cancer.
[0066] In the present description, the expression "measured in
vitro" means that the expression level is not known (it cannot be
merely retrieved from a database) and has to be physically measured
by some treatment step, which is performed in a laboratory. The
term "primer", as used herein, refers to an oligonucleotide,
whether occurring naturally (as in a purified restriction digest)
or produced synthetically, and which is capable of initiating
synthesis of a strand complementary to a nucleic acid when placed
under appropriate conditions, i.e., in the presence of nucleotides
and an inducing agent, such as a DNA polymerase, and at a suitable
temperature and pH. The primer may be either single-stranded or
double-stranded and must be sufficiently long to prime the
synthesis of the desired extension product in the presence of the
inducing agent. The exact length of the primer will depend upon
many factors, including temperature, sequence and/or homology of
primer and the method used. For example, in diagnostic
applications, the oligonucleotide primer typically contains 10 to
25 or more nucleotides, depending upon the complexity of the target
sequence, although it may contain fewer nucleotides.
Method for Producing Cancer Stem Cells
[0067] In the context of the present invention, the inventors have
found that .DELTA.133p53.beta. isoform (and also
.DELTA.133p53.gamma. to a lesser extent), but not
.DELTA.133p53.alpha. isoform (also referred to as .DELTA.133p53
isoform), is not only a marker of a risk of cancer metastasis, but
actually promotes cancer stem cell phenotype. In particular,
expression of .DELTA.133p53.beta. isoform (and also
.DELTA.133p53.gamma. to a lesser extent), but not of
.DELTA.133p53.alpha. isoform (also referred to as .DELTA.133p53
isoform), promotes cancer cell sphere-forming activity, and also
promotes Sox 2, Oct 3/4 and Nanog expression (but not c-Myc),
transcription factors known to be useful of reprogramming cells
towards pluripotency.
[0068] This finding is very important since it provides a mean for
producing high numbers of CSCs, thus permitting to study and better
understand their biology, a crucial point for improving anticancer
therapies.
[0069] In a first aspect, the present invention thus relates to a
method for producing cancer stem cells, comprising: [0070] a)
transducing cancer cells with a vector expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; [0071] b)
culturing transduced cancer cells in a medium supporting expansion
of transduced cancer cells; and [0072] c) isolating cancer stem
cells.
Cancer Cells
[0073] In the method for producing cancer stem cells of the present
invention, cancer cells are preferably selected from the group of
solid cancer cells, and in particular from the group consisting of
breast cancer cells, colorectal cancer cells ovarian cancer cells,
digestive cancers cells (also referred as gastrointestinal cancer
including colorectal cancer, oesophageal cancer, gastric cancer,
pancreatic cancer, hepatocellular carcinoma, cholangiocellular
cancer and teratocarcinoma), pancreatic cancer cells and throat
cancer cells, particularly of human subject, more preferably cancer
cells are selected from breast cancer cells colorectal cancer
cells, gastrointestinal cancer cells, lung cancer cells and
prostate cancer cells and even more preferably cancer cells are
breast cancer cells or colorectal cancer cells.
[0074] Moreover, the cancer cells may be selected from the group of
hematopoietic cancer cells, and in particular from the group
consisting of leukaemia cells and lymphoma cells. Preferably, the
hematopoietic cancer cells are human hematopoietic cancer
cells.
[0075] It is known in the art that many types of cancer cells, when
transduced by at least one and preferably several of Yamanaka
factors (Oct 3/4, Nanog, Sox 2 and c-Myc), may give rise to CSCs.
Examples of cancer cells in which this has been shown include:
[0076] colon (or colorectal) cancer cells (see for instance Oshima
et al (2014), which describes that colon cancer cells transduced
with factors Oct 3/4, Sox 2 and KLF4 showed significantly enhanced
CSCs proprieties in terms of marker gene expression and sphere
formation), [0077] gastrointestinal cancer cells (including cells
of colorectal cancer, oesophageal cancer, gastric cancer,
pancreatic cancer, hepatocellular carcinoma, cholangiocellular
cancer and teratocarcinoma). Miyoshi et al (2010) disclose that
cells obtained from the above cited gastrointestinal cancers
induced with Nanog transcriptional factor manifest a pluripotency
like CSCs, [0078] lung cancer cells (see Chiou et al., 2010, which
describes that ectopic expression of Oct4 and Nanog transcriptional
factors in lung adenocarcinoma cells induce the sphere formation),
and [0079] prostate cancer cells (see Jeter et al, 2011, which
describes that tetracycline-inducible Nanog-overexpression in
prostate cancer cell lines promotes tumour regeneration by
enhancing the expression of several CSCs associated molecules.
[0080] Since transduction with .DELTA.133p53.beta. isoform or
.DELTA.133p53.gamma. isoform induces the expression of Sox 2, Nanog
and Oct 3/4, its transduction in any cancer cell known to give rise
to CSCs when transduced by at least one and preferably several of
Yamanaka factors (Oct 3/4, Nanog, Sox 2 and c-Myc) is expected to
generate CSCs. This has been demonstrated by the inventors for two
distinct types of cancer cells: breast and colon cancer cells. Such
cancer cells may be obtained from any cancer sample, including a
cancer biopsy, a complete or partial cancer surgical resection, or
a blood sample. Indeed, cancer cells (including cancer stem cells)
are well known to circulate in blood (Mavroudis-2010;
Alix-Panabieres et al., 2013).
Isoform
[0081] In a preferred embodiment of the method for producing cancer
stem cells according to the invention, it is the
.DELTA.133p53.beta. isoform or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms (preferably only the
.DELTA.133p53.beta. isoform) that is/are transduced in cancer cells
in step b). Indeed, expression of .DELTA.133p53.beta. isoform is
particularly associated to induction of cancer stem cells.
Vector Expressing .DELTA.133p538 Isoform, .DELTA.133p53.gamma.
Isoform, or Both .DELTA.133p538 and .DELTA.133p53.gamma. Isoforms
(Step b)
[0082] Any appropriate vector expressing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms may be used.
[0083] A suitable vector comprises a nucleic acid molecule encoding
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms and elements
necessary to allow expression thereof.
[0084] Suitable vectors notably include plasmid vectors and viral
vectors.
[0085] Viral vectors can be replication-competent or -selective
(e.g. engineered to replicate better or selectively in specific
host cells), or can be genetically disabled so as to be
replication-defective or replication-impaired. Typically, such
vectors are commercially available (e.g. in Invitrogen, Stratagene,
Amersham Biosciences, Promega, etc.) or available from depositary
institutions such as the American Type Culture Collection (ATCC,
Rockville, Md.) or have been the subject of numerous publications
describing their sequence, organization and methods of producing,
allowing the artisan to apply them.
[0086] In an embodiment, a plasmid vector expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is used.
[0087] Representative examples of suitable plasmid vectors include,
without limitation, pREP4, pCEP4 (Invitrogen), pCI (Promega), pVAX
(Invitrogen) and pGWiz (Gene Therapy System Inc).
[0088] For transduction, a plasmid vector may be complexed to
lipids or polymers to form particulate structures such as
liposomes, lipoplexes or nanoparticles.
[0089] In a preferred embodiment, a viral vector expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is used (i.e
a viral vector comprising a nucleic acid molecule encoding
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms and elements
necessary to allow expression thereof).
[0090] Representative examples of suitable viral vectors are
generated from a variety of different viruses (e.g. retrovirus,
adenovirus, adenovirus-associated virus (AAV), poxvirus, herpes
virus, measles virus, foamy virus, alphavirus, vesicular stomatis
virus, etc). As described above, the term "viral vector"
encompasses vector DNA, genomic DNA as well as viral particles
generated thereof, and especially infectious viral particles.
[0091] In a preferred embodiment, a retroviral vector expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms isoform is
used (i.e a retroviral vector comprising a nucleic acid molecule
encoding .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms and
elements necessary to allow expression thereof).
[0092] Retroviruses have the property of infecting, and in most
cases integrating into, dividing cells and in this regard are
particularly appropriate for use in the context of the present
invention for producing cancer stem cells. A suitable retrovirus
generally contains the LTR sequences, an encapsidation region and a
nucleic acid molecule encoding .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform. The recombinant retrovirus can be
derived from a retrovirus of any origin (murine, primate, feline,
human, etc.) and in particular from the MoMuLV (Moloney murine
leukemia virus), MVS (Murine sarcoma virus), Friend murine
retrovirus (Fb29), Murine Embryonic Stem Cell Virus (MESV), LN
virus or Murine Stem Cell Virus (MSCV). It is propagated in an
encapsidation cell line which is able to supply in trans the viral
polypeptides gag, pol and/or env which are required for
constituting a viral particle. Such cell lines are described in the
literature (PA317, Psi CRIP GP+Am-12, HEK 293T etc.). The
retroviral vector according to the invention can contain
modifications, in particular in the LTRs (replacement of the
promoter region with a eukaryotic promoter) or the encapsidation
region (replacement with a heterologous encapsidation region).
[0093] In a particularly preferred embodiment, the vector used for
transducing cancer cells in step b) is a Murine Stem Cell Virus
(MSCV), which is derived from the Murine Embryonic Stem Cell Virus
(MESV) and the LN retroviral vectors (Grez, M., et al. 1990;
Miller, A. D. et al. 1989). Notably, the transducing vector may be
obtained by cloning a molecule encoding .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms into a pMSCV vector
commercialized by Clontech, such as pMSCVhyg, pMSCVneo, or
pMSCVpuro.
[0094] However, other types of viral vectors expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms may be
used.
[0095] Examples of viral vectors that are useful in the context of
the invention include adenoviral vectors, which may be derived from
a variety of human or animal sources (e.g. canine, ovine, simian
adenovirus, etc). Any serotype can be employed with a special
preference for human adenoviruses and a specific preference for
subgenus C such as Ad2, Ad5, Ad6, and subgenus B such as Ad11, Ad34
and Ad35. The cited adenovirus are available from ATCC or have been
the subject of numerous publications describing their sequence,
organization and methods of producing, allowing the artisan to
apply them. When an adenoviral vector is used, it is preferably an
E1-defective adenoviral vector with an E1 deletion extending from
approximately positions 459 to 3328 or from approximately positions
459 to 3510 (by reference to the sequence of Ad5 disclosed in the
GenBank under the accession number M73260.1). The cloning capacity
can further be improved by deleting additional portion(s) of the
adenoviral genome (all or part of the non-essential E3 region (e.g.
deletion from approximately positions 27867 to 30743) or of other
essential E2 and/or E4 regions. The nucleic acid molecule encoding
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms can then be
inserted in any location of the adenoviral genome, with a specific
preference for insertion in replacement of the E1 and/or E3 region.
They may be positioned in sense or antisense orientation relative
to the natural transcriptional direction of the region in
question.
[0096] Other examples of viral vectors that may be used in the
context of the invention include poxvirus vectors such as fowlpox
vectors (e.g. FP9), canarypox vectors (e.g. ALVAC) and vaccinia
virus vectors, the latter being preferred. Suitable vaccinia
viruses include without limitation the Copenhagen strain, the Wyeth
strain, NYVAC and the modified Ankara (MVA) strain. The general
conditions for constructing and producing recombinant poxvirus are
well known in the art. The nucleic acid molecule encoding
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is preferably
inserted within the poxviral genome in a non-essential locus.
Thymidine kinase gene is particularly appropriate for insertion in
Copenhagen vaccinia vectors and deletion II or III for insertion in
MVA vector.
[0097] Other viral vectors suitable in the context of the invention
are morbillivirus which can be obtained from the paramyxoviridae
family, with a specific preference for measles virus. Insertion of
the nucleic acid molecule encoding .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms between P and M genes or between H
and L genes is particularly appropriate.
[0098] In the above vectors, the nucleic acid molecule encoding
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms are in a form
suitable for expression in cancer cells, which means that each of
the nucleic acid molecules set forth herein is operably linked to
appropriate regulatory sequences.
[0099] It will be appreciated by those skilled in the art that the
choice of the regulatory sequences can depend on such factors as
the vector itself and the cancer cells to be transduced, and will
be easily selected by those skilled in the art based on common
general knowledge and publications on this topic. Suitable
promoters for constitutive expression in eukaryotic systems include
viral promoters, such as SV40 promoter, the cytomegalovirus (CMV)
immediate early promoter or enhancer, the adenovirus early and late
promoters, the thymidine kinase (TK) promoter of herpes simplex
virus (HSV)-1 and retroviral long-terminal repeats (e.g. MoMuLV and
Rous sarcoma virus (RSV) LTRs) as well as cellular promoters such
as the phosphoglycero kinase (PGK) promoter. Examples of suitable
promoters for a Murine Stem Cell Virus (MSCV) vector include those
present in pMSCV vector commercialized by Clontech, such as
pMSCVhyg, pMSCVneo, or pMSCVpuro.
Culture of Transduced Cancer Cells (Step b)
[0100] In step b), transduced cancer cells are cultured in a medium
supporting their expansion. Such a medium may be a basal medium
(comprising inorganic salts, amino acids, vitamins and glucose,
such as DMEM), which may be supplemented with a reducing agent
(such as .beta.-mercaptoethanol), at least one antibiotic (such as
Penicillin-Streptomycin), and/or at least one growth factor able to
sustain expansion of the type of cancer cells transduced
(including, but not limited to, Epidermal Growth Factor (EGF)
and/or basic Fibroblast Growth Factor (bFGF)).
[0101] For breast cancer cells and more generally cancer cells of
epithelial origin (cancer cells derived from a carcinoma), a
preferred medium in step b) may contain a basal medium comprising
inorganic salts, amino acids, vitamins and glucose,
.beta.-mercaptoethanol, at least one antibiotic, and bFGF.
[0102] Step b) is performed for a period sufficient in order to
recover cancer stem cells from the transduced cancer cell culture.
A suitable period should be optimized for each type of cancer
cells, but will generally be between 3 and 21 days, in particular
between 7 and 14 days.
Isolation of Cancer Stem Cells (Step c)
[0103] In step c), cancer stem cells are isolated from the
transduced cancer cells culture.
[0104] In the transduced cancer cells culture, cancer stem cells
may be isolated based on selection of any feature specific to
cancer stem cells compared to other cancer cells.
[0105] In particular, depending on the type of cancer cells, CSCs
can be identified and isolated by means of at least one of the 4
following methods: [0106] i) isolation according to CSC-specific
cell surface markers; [0107] ii) isolation by flow cytometry based
on side-population (SP) phenotype by DNA dye exclusion; [0108] iii)
isolation by flow cytometry based on high aldehyde dehydrogenase
(ALDH) activity; and [0109] iv) submission to sphere-forming assay
and collection of spheres.
[0110] The suitability of the four above mentioned methods may
notably be determined by those skilled in the art depending on the
type of cancer cells based on information provided above in the
definitions of cancer stem cells (and in particular in Tables 2a
and 2b).
[0111] In method i), CSCs are isolated based on CSC-specific cell
surface markers. In this method, transduced cancer cells are
stained using antibodies directed to one or more CSC-specific cell
surface markers, and cells having the desired surface marker
phenotype are sorted. Those skilled in the art know how to
implement such siolation based on surface cell markers. For
instance, flow cytometry cell-sorting may be used, transduced
cancer cells are directly or indirectly fluorescently stained with
antibodies directed to one or more CSC-specific cell surface
markers and cells by detected by flow cytometer laser as having the
desired surface marker phenotype are sorted. In another embodiment,
magnetic separation may be used. In this case, antibody labelled
transduced cancer cells (which correspond to CSCs if an antibody
directed to a CSC marker is used, or to non-CSC if an antibody
specifically not expressed by CSCs is used) are contacted with
magnetic beads specifically binding to the antibody (for instance
via avidin/biotin interaction, or via antibody-antigen binding) and
separated from antibody non-labelled transduced cancer cells.
Several rounds of magnetic purification may be used based on
markers specifically expressed and non-expressed by CSCs.
[0112] In method ii), CSCs are isolated by flow cytometry
cell-sorting based on DNA dye side population (SP) phenotype. This
method is based on the passive uptake of cell-permeable DNA dyes by
live cells and pumping out of such DNA dyes by a side population of
stem cells via ATP-Binding Cassette (ABC) transporters allowing the
observation of a side population that has a low DNA dye
fluorescence at the appropriate wavelength. ABC pumps can be
specifically inhibited by drugs such as verapamil (100 .mu.M final
concentration) or reserpine (5 .mu.M final concentration), and
these drugs may be used to generate control samples, in which no SP
phenotype may be detected. Appropriate cell-permeable DNA dyes that
may be used include Hoechst 33342 (the main used DNA dye for this
purpose, see Golebiewska et al., 2011) and Vybrant.RTM.
DyeCycle.TM. stains available in various fluorescences (violet,
green, and orange; see Telford et al-2010).
[0113] In method iii), CSCs are isolated by flow cytometry
cell-sorting based on high ALDH activity. Indeed, several types of
CSCs have been characterized as displaying high ALDH activity. In
this method, transduced cancer cells are incubated with a
fluorescent ALDH substrate, which freely diffuses into intact and
viable cells (such as the BODIPY.TM.-aminoacetaldehyde (BAAA)
reagent of ALDEFLUOR.TM. kit commercialized by Stemcell
Technologies). In the presence of ALDH, this fluorescent substrate
is converted into a fluorescent metabolite (such as the
BODIPY'-anninoacate (BAA) reagent obtained from BODIPY.TM.-BAAA in
the ALDEFLUOR.TM. kit commercialized by Stemcell Technologies),
which is retained inside the cells. The amount of fluorescent
reaction product is proportional to the ALDH activity in the cells
and is measured using a flow cytometer. Viable ALDH.sup.bright
(ALDH.sub.br) cells can, in principle, be isolated using a cell
sorter. Active efflux of the reaction product is inhibited by an
efflux inhibitor in the ALDEFLUOR.TM. Assay Buffer. A specific
inhibitor of ALDH, such as diethylaminobenzaldehyde (DEAB), is used
to control for background fluorescence.
[0114] In method iv), CSCs are isolated by submitting transduced
cancer cells to sphere-forming assay and collecting spheres. This
method relies on the preferential ability of cancer stem cells to
form spheres under serum-free (and preferably low adherence)
culture conditions, whereas bulk tumor cells are less likely to be
able to form spheres under the same conditions. A suitable
sphere-forming assay for isolation of CSCs may comprise: [0115] 1)
resuspending transduced cancer cells into a serum-free medium,
preferably in the presence of specific growth factors (including,
but not limited to, Epidermal Growth Factor (EGF) and basic
Fibroblast Growth Factor (bFGF)), and plating them into tissue
culture dishes, to which mammalian cells preferably poorly adhere;
[0116] 2) incubating the cancer cells during 5 to 20 days; and
[0117] 3) collecting spheres.
[0118] In step 1), cancer cells are resuspended into a serum-free
medium (e.g., MammoCult.RTM., available from StemCell Technologies,
Inc., Vancouver, Canada), preferably in the presence of specific
growth factors such as EGF and bFGF, and plated into tissue culture
dishes. Preferably, tissue culture dishes to which mammalian cells
poorly adhere are selected (e.g. Ultra Low Cluster Plate, 24-well,
Flat Bottom from Corning Inc). In this step, the seeding density is
preferably kept between 250 and 2500 cells/cm.sup.2, and is
preferably optimized for each type of cancer cells.
[0119] For instance, for breast cancer cells in MammoCult.TM.
Medium enriched with MammoCult.TM. Proliferation Supplements,
hydrocortisone and heparin (Stem Cell Technologies), a seeding
density of 500 cells/well of Ultra Low Cluster Plate, 24-well, Flat
Bottom (Corning Inc) is appropriate.
[0120] In step 2), cancer cells are incubated, preferably at about
37.degree. C. under 5% CO.sub.2 atmosphere, during 5 to 20 days,
preferably during 7 to 15 days.
[0121] Finally, in step 3), spheres at least 50 .mu.m large that
have formed during incubation are collected.
[0122] The isolated CSCs obtained using one of the above described
methods may be then optionally be tested by using a
xenotransplantation test. In this case, the isolated subpopulation
of CSCs is submitted to serial transplantations into
immunocompromised mice (for example SCID mice, see Schatton et al.,
2009) or zebrafishes (see Dovey et al., 2009), preferably into
immunocompromised mice (for example SCID mice). After
transplantation of the CSCs population, the resulting tumor is
expected to mirror the phenotypic heterogeneity of the original
tumor and contain CSCs with preserved ability to self-renew in
subsequent serial transplantations (Le Cheng, 2009).
Preferred Embodiments
[0123] Various preferred specific features corresponding to various
generic elements of the method for producing cancer stem cells
according to the invention have been described above in the section
specifically relating to this element. In the context of the
invention, each list of appropriate features for a particular
element and each specific feature disclosed for a particular
element may be combined with any generic other element, list of
appropriate features for said other element or any specific feature
disclosed for said other element.
[0124] In particular, preferred embodiments of an element of the
method for producing cancer stem cells according to the invention
may be combined with any generic other element or with preferred
embodiments of said other element.
[0125] Preferred embodiments correspond to those in which at least
one element is limited to a preferred embodiment, as listed in
Table 3 below:
TABLE-US-00004 TABLE 3 Preferred embodiment of various elements of
the method for producing cancer stem cells according to the
invention. Element Preferred embodiment(s) Cancer cell Breast
cancer cell or colorectal cancer cells P53 isoform transduced in
.DELTA.133p53.beta. isoform or .DELTA.133p53.beta. cancer cells and
.DELTA.133p53.gamma. isoforms, preferably .DELTA.133p53.beta.
isoform Type of vector used for transducing Retroviral vector,
preferably Murine .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
Stem Cell Virus (MSCV) vector isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms Medium for culture of transduced
basal medium comprising inorganic cancer cells salts, amino acids,
vitamins and glucose, .beta.-mercaptoethanol, at least one
antibiotic, and bFGF Collection of cancer stem cells Selection
based on surface markers or sphere-forming ability.
[0126] In a particularly preferred embodiment of the method for
producing cancer stem cells according to the invention, cancer
cells used for transduction are breast cancer cells, the P53
isoform transduced in cancer cells is .DELTA.133p53.beta. isoform
and is transduced using a Murine Stem Cell Virus (MSCV) vector, the
medium used in step b) is a basal medium comprising inorganic
salts, amino acids, vitamins and glucose, .beta.-mercaptoethanol,
at least one antibiotic, and bFGF, and cancer stem cells are
isolated in step c) by selection based on surface markers or
sphere-forming ability.
Prediction of the Risk that a Chemotherapeutic Anti-Cancer
Treatment Induces Cancer Stem Cells in a Subject Suffering from
Cancer
[0127] The inventors further surprisingly found that anticancer
treatment of cancer cells expressing .DELTA.133p53.beta. isoform by
etoposide (a topoisomerase II inhibitor) is not only inefficient
(resistance to treatment) but further promotes cancer sternness by
increasing .DELTA.133p53.beta. expression level. As a result,
treating cancer patients with .DELTA.133p53.beta.-expressing would
promote CSC formation and would thus be rather deleterious than
useful.
[0128] The present invention thus also relates to a method for
predicting the risk that treatment with a chemotherapeutic
anti-cancer agent induces cancer stem cells in a subject suffering
from cancer from a cancer sample of said subject, comprising:
[0129] a) measuring in vitro the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample, untreated with the chemotherapeutic anti-cancer
agent; [0130] b) treating said cancer sample with said
chemotherapeutic anti-cancer agent; [0131] c) measuring in vitro
the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in the treated cancer sample; [0132]
d) comparing the values obtained in steps a) and c); and [0133] e)
concluding to: [0134] (i) the presence of a significant risk that
treatment with said chemotherapeutic anti-cancer agent induces
cancer stem cells in said subject if the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms measured in
step c) is higher than the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms measured in step a), or [0135]
(ii) the absence of a significant risk that treatment with said
chemotherapeutic anti-cancer agent induces cancer stem cells in
said subject if the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms measured in step c) is lower than
or equal to the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms measured in step a).
Chemotherapeutic Anti-Cancer Treatment
[0136] In the method of prediction of the risk that a
chemotherapeutic anti-cancer treatment induces cancer stem cells
according to the invention, the chemotherapeutic anti-cancer agent
susceptible to induce cancer stem cells in a cancer subject is
preferably selected from: [0137] a topoisomerase II inhibitor,
including etoposide, etoposide, tenoposide, doxorubicine,
daunorubicin, mitoxantrone, and amsacrine; [0138] an anti-tubuline
agent, including taxanes such as paclitaxel and docetaxel, and
vinca alkaloids such as vinblastine, vincristine, vindesine, and
vinorelbine; [0139] antimetabolites, including pyrimidine analogue
5-Fluorouracil (5-FU).
[0140] In a preferred embodiment, the chemotherapeutic anti-cancer
treatment susceptible to induce cancer stem cells in a cancer
subject is a topoisomerase II inhibitor, in particular selected
from etoposide, tenoposide, doxorubicine, daunorubicin,
mitoxantrone, and amsacrine. More preferably, the chemotherapeutic
anti-cancer treatment susceptible to induce cancer stem cells in a
cancer subject is etoposide.
Cancer and Cancer Sample
[0141] In the method of prediction of the risk that a
chemotherapeutic anti-cancer treatment induces cancer stem cells
according to the invention, the cancer from which the subject is
suffering is preferably selected from the group of solid cancers,
and in particular from the group consisting of breast cancer,
colorectal cancer, ovarian cancer, digestive cancers (also referred
as gastrointestinal cancer, including colorectal cancer,
oesophageal cancer, gastric cancer, pancreatic cancer,
hepatocellular carcinoma, cholangiocellular cancer and
teratocarcinoma), pancreatic cancer, lung cancer, prostate cancer
and throat cancer, particularly of human subject, more preferably
breast cancer colorectal cancer, gastrointestinal cancer, lung
cancer and prostate cancer and even more preferably the cancer from
which the subject is breast cancer or colorectal cancer.
[0142] Moreover, the cancer may be selected from the group of
hematopoietic cancers, and in particular from the group consisting
of leukaemias and lymphomas. Preferably, the hematopoietic cancer
is a human hematopoietic cancer.
[0143] It is known in the art that many types of cancer cells, when
transduced by at least one and preferably several of Yamanaka
factors (Oct 3/4, Nanog, Sox 2 and c-Myc), may give rise to CSCs.
Examples of cancer cells in which this has been shown include:
[0144] colon (or colorectal) cancer cells (see for instance Oshima
et al (2014), which describes that colon cancer cells transduced
with factors Oct 3/4, Sox 2 and KLF4 showed significantly enhanced
CSCs proprieties in terms of marker gene expression and sphere
formation), [0145] gastrointestinal cancer cells (including cells
of colorectal cancer, oesophageal cancer, gastric cancer,
pancreatic cancer, hepatocellular carcinoma, cholangiocellular
cancer and teratocarcinoma). Miyoshi et al (2010) disclose that
cells obtained from the above cited gastrointestinal cancers
induced with Nanog transcriptional factor manifest a pluripotency
like CSCs, [0146] lung cancer cells (see Chiou et al., 2010, which
describes that ectopic expression of Oct4 and Nanog transcriptional
factors in lung adenocarcinoma cells induce the sphere formation),
and [0147] prostate cancer cells (see Jeter et al, 2011, which
describes that tetracycline-inducible Nanog-overexpression in
prostate cancer cell lines promotes tumour regeneration by
enhancing the expression of several CSCs associated molecules.
[0148] Since transduction with .DELTA.133p53.beta. isoform or
.DELTA.133p53.gamma. isoform induces the expression of Sox 2, Nanog
and Oct 3/4, its transduction in any cancer cell known to give rise
to CSCs when transduced by at least one and preferably several of
Yamanaka factors (Oct 3/4, Nanog, Sox 2 and c-Myc) is expected to
generate CSCs. This has been demonstrated by the inventors for two
distinct types of cancer cells: breast and colon cancer cells.
[0149] The cancer sample from which the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is measured
in step a) may be a cancer biopsy or a complete or partial cancer
surgical resection. Alternatively, the cancer sample from which the
expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is measured in step a) may be a blood
sample. Indeed, cancer cells (including cancer stem cells) are well
known to circulate in blood (Mavroudis-2010; Alix-Panabieres et
al., 2013), and expression of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms may thus also be detected in a blood
sample of a cancer patient. The skilled artisan knows from Anensen
et al. (2006) that p53 isoforms may be measured in the blood.
Isoform
[0150] In a preferred embodiment of the method of prediction of the
risk that a chemotherapeutic anti-cancer treatment induces cancer
stem cells according to the invention, it is the expression level
of .DELTA.133p53.beta. isoform or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms that is measured in step a). Indeed,
expression of .DELTA.133p53.beta. isoform is particularly
associated to induction of cancer stem cells in a cancer subject
treated with a chemotherapeutic anti-cancer treatment.
Steps a) and c)-- Measure of the Expression Level of .DELTA.133p538
Isoform, .DELTA.133p53.gamma. Isoform, or Both .DELTA.133p538 and
.DELTA.133p53.gamma. Isoforms in Untreated (Step a)) or Treated
(Step c)) Cancer Cells
[0151] In step a), the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms is measured in vitro in a cancer
sample from the subject that has not been treated with the
chemotherapeutic anti-cancer agent.
[0152] In step c), the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms is measured in vitro in the
cancer sample from the subject, which has been further treated with
the chemotherapeutic anti-cancer agent.
[0153] In some embodiments, the method of prediction of the risk
that a chemotherapeutic anti-cancer treatment induces cancer stem
cells according to the invention may further comprise a preliminary
step al) of taking a cancer sample from the subject.
[0154] In addition, step a), step c) or both may further comprise
preliminary substeps of transformation of the untreated and treated
cancer sample, which may vary depending if the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is measured
at the protein or nucleic acid level.
[0155] Since the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms has to be measured in a cancer sample
of the subject both before and after treatment with the
chemotherapeutic anti-cancer agent, and since the measure may
involve preliminary substeps of transformation of the untreated and
treated cancer sample, the initial cancer sample may be divided in
several parts, one part being used for measuring the expression
level of .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
before treatment with the chemotherapeutic anti-cancer agent in
step a), another part being used for measuring the expression level
of .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms after
treatment with the chemotherapeutic anti-cancer agent in step c).
The initial cancer sample will then be divided so that all parts be
as much similar as possible (number and types of cells present in
the sample), in order to prevent or reduce to the minimal any bias
due to sampling.
Measure at the Protein Level
[0156] In an embodiment of the method of prediction of the risk
that a chemotherapeutic anti-cancer treatment induces cancer stem
cells according to the invention, the expression levels of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
untreated and treated cancer sample are measured at the protein
level.
[0157] In this case, preliminary substeps of transformation of the
untreated and treated cancer sample may include a substep of
extraction of proteins present in the cancer sample, for further
measure of the amount of .DELTA.133p53B, .DELTA.133p53.gamma., or
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. proteins in the
cancer sample protein extract. Methods for extracting proteins from
a cell or tissue sample are well known to those skilled in the art.
Such preliminary substep of extracting proteins is nevertheless not
necessary when some particular technologies able to measure the
amount of a particular protein directly in a cell or tissue sample
are used.
[0158] When the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in said untreated and treated cancer
sample is measured at the protein level, any appropriate technology
known to those skilled in the art for measuring protein expression
levels may be used. Suitable technologies include enzyme-linked
immunosorbent assays (ELISAs), Western blots, immunoprecipitations,
immunohistochemistry, and immunofluorescence.
[0159] Most of suitable technologies use an antibody able to bind
to .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms. Such
antibody may specifically bind to .DELTA.133p53.beta. isoform
(anti-.DELTA.133p53.beta. antibody) and/or to .DELTA.133p53.gamma.
isoform (anti-.DELTA.133p53.gamma. antibody), or may recognize
several p53 isoforms, including the .DELTA.133p53.beta. isoform,
the .DELTA.133p53.gamma. isoform, or both the .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms. When performed at the protein
level, step a) is thus preferably performed by an immunoassay using
an antibody able to bind to .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms, such as an antibody binding to
.DELTA.133p53.beta. and/or .DELTA.133p53.gamma. isoform and to
other p53 isoforms, an anti-.DELTA.133p53.beta. antibody or an
anti-.DELTA.133p53.gamma. antibody. The antibody can be a
polyclonal antibody or a monoclonal antibody, although monoclonal
antibodies are preferred. Preferably, said antibody is
labelled.
[0160] When an antibody binding to .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms and to other p53 isoforms (including
an antibody binding all p53 isoforms) is used, the relative amount
of .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform may be
determined using western blot analysis, based on the distinct
molecular weights of the various p53 isoforms (see FIG. 1A). Such
antibody binding to .DELTA.133p53.beta. and/or .DELTA.133p53.gamma.
isoform and to other p53 isoforms are commercially available, such
as the p53 (D0-1): sc-126 antibody recognizing amino acids 11-25 of
human p53 available from Santa Cruz Biotechnology.
[0161] Using an anti-.DELTA.133p53.beta. or
anti-.DELTA.133p53.gamma. specific antibody, detection may be
accomplished using any of a variety of immunoassays.
[0162] For example, by radioactively labelling an antibody, it is
possible to detect the antibody through the use of radioimmune
assays. A description of a radioimmune assay (RIA) may be found in
Laboratory Techniques and Biochemistry in Molecular Biology, by
Work T. S. et al., North Holland Publishing Company, NY (1978),
with particular reference to the chapter entitled "An Introduction
to Radioimmune Assay and Related Techniques" by Chard T. The
radioactive isotope can be detected by such means as the use of a
gamma counter or a scintillation counter or by audioradiography.
Isotopes which are particularly useful for the purpose of the
present invention are: .sup.3H, .sup.131I, .sup.35S, 14C, and
preferably .sup.125I.
[0163] It is also possible to label an antibody with a fluorescent
compound. When the fluorescently labelled antibody is exposed to
light of the proper wave length, its presence can then be detected
due to fluorescence. Among the most commonly used fluorescent
labelling compounds are fluorescein isothiocyanate, rhodamine,
phycoerytherin, phycocyanin, allophycocyanin, ophthaldehyde and
fluorescamine.
[0164] An antibody can also be detectably labelled using
fluorescence emitting metals such as .sup.152Eu, or others of the
lanthanide series. These metals can be attached to the antibody
using such metal chelating groups as diethylenetriaminepentaacetic
acid (DTPA) or ethylenedianninetetraacetic acid (EDTA).
[0165] An antibody can also be detectably labelled by coupling it
to a chemiluminescent compound. The presence of the
chemiluminescent-tagged antibody is then determined by detecting
the presence of luminescence that arises during the course of a
chemical reaction. Examples of particularly useful chemiluminescent
labelling compounds are luminol, luciferin, isoluminol, theromatic
acridinium ester, imidazole, acridinium salt and oxalate ester.
[0166] Likewise, a bioluminescent compound may be used to label an
antibody of the present invention. Bioluminescence is a type of
chemiluminescence found in biological systems in which a catalytic
protein increases the efficiency of the chemiluminescent reaction.
The presence of a bioluminescent protein is determined by detecting
the presence of luminescence. Important bioluminescent compounds
for purposes of labelling are luciferin, luciferase and
aequorin.
[0167] In the detection assays of the invention, the amount of
binding of the antibody to the biological sample can be determined
by the intensity of the signal emitted by the labelled antibody
and/or by the number cells in the biological sample bound to the
labelled antibody.
[0168] The detection or the expression level of .DELTA.133p53.beta.
or .DELTA.133p53.gamma. isoform in a cancer sample may notably be
determined by a radioimmunoassay (RIA), an immunoradiometric assay
(IRMA), and/or an enzyme immunoassay (such as Enzyme-Linked
Immunosorbent Assay (ELISA)).
[0169] "Radioimmunoassay" is a technique for detecting and
measuring the concentration of an antigen using a radioactively
labelled form of the antigen (i.e. .DELTA.133p53.beta. or
.DELTA.133p53.gamma. polypeptide). Examples of radioactive labels
for antigens include .sup.3H, .sup.14C, and .sup.125I. The
concentration of the antigen (.DELTA.133p53.beta. or
.DELTA.133p53.gamma. polypeptide) in a biological sample is
measured by having the non-labelled antigen in the sample compete
with a radioactively labelled antigen for binding to an antibody to
the antigen (anti-.DELTA.133p53.beta. or anti-.DELTA.133p53.gamma.
antibody). To ensure competitive binding between the labelled
antigen and the unlabeled antigen, the labelled antigen is present
in a sufficient concentration to saturate the binding sites of the
antibody. The higher the concentration of antigen in the sample,
the lower the concentration of labelled antigen that will bind to
the antibody will be.
[0170] In a radioimmunoassay, to determine the concentration of
labelled antigen bound to an antibody, the antigen-antibody complex
must be separated from the free antigen. One method for separating
the antigen-antibody complex from the free antigen is by
precipitating the antigen-antibody complex with an anti-isotype
antiserum. Another method for separating the antigen-antibody
complex from the free antigen is by precipitating the
antigen-antibody complex with formalin-killed S. aureus. Yet
another method for separating the antigen-antibody complex from the
free antigen is by performing a "solid-phase radioimmunoassay"
where the antibody is linked (i.e. covalently) to Sepharose beads,
polystyrene wells, polyvinylchloride wells, or microtiter wells. By
comparing the concentration of labelled antigen bound to antibody
to a standard curve based on samples having a known concentration
of antigen, the concentration of antigen in the biological sample
can be determined.
[0171] An "Immunoradiometric assay" (IRMA) is an immunoassay in
which the antibody reagent is radioactively labelled. An IRMA
requires the production of a multivalent antigen conjugate by
techniques such as conjugation to a protein e.g., rabbit serum
albumin (RSA). The multivalent antigen conjugate must have at least
2 antigen residues per molecule and the antigen residues must be of
sufficient distance apart to allow binding by at least two
antibodies to the antigen. For example, in an IRMA the multivalent
antigen conjugate can be attached to a solid surface such as a
plastic sphere. Unlabelled "sample" antigen and radioactively
labelled antibody to antigen are added to a test tube containing
the multivalent antigen conjugate coated sphere. The antigen in the
sample competes with the multivalent antigen conjugate for antigen
antibody binding sites. After an appropriate incubation period, the
unbound reactants are removed by washing and the amount of
radioactivity on the solid phase is determined. The amount of bound
radioactive antibody is inversely proportional to the concentration
of antigen in the sample.
[0172] The most common enzyme immunoassay is the "Enzyme-Linked
Immunosorbent Assay (ELISA)". The "Enzyme-Linked Immunosorbent
Assay (ELISA)" is a technique for detecting and measuring the
concentration of an antigen using a labelled (i.e. enzyme linked)
form of the antibody.
[0173] In a "sandwich ELISA", an antibody (anti-.DELTA.133p53.beta.
or anti-.DELTA.133p53.gamma. antibody) is linked to a solid phase
(i.e. a microtiter plate) and exposed to a biological sample
containing antigen (.DELTA.133p53.beta. or .DELTA.133p53.gamma.
polypeptide). The solid phase is then washed to remove unbound
antigen. An enzyme-linked antibody to the antigen is then bound to
the bound-antigen (if present) forming an antibody-antigen-antibody
sandwich. Examples of enzymes that can be linked to the antibody
are alkaline phosphatase, horseradish peroxidase, luciferase,
urease, and 3-galactosidase. The enzyme linked antibody reacts with
a substrate to generate a colored reaction product that can be
assayed for.
[0174] In a "competitive ELISA", an antibody
(anti-.DELTA.133p53.beta. or anti-.DELTA.133p53.gamma. antibody) is
incubated with a sample containing antigen (.DELTA.133p53.beta. or
.DELTA.133p53.gamma. polypeptide). The antigen-antibody mixture is
then contacted with an antigen-coated solid phase (i.e. a
microtiter plate). The more antigen present in the sample, the less
free antibody that will be available to bind to the solid phase. An
enzyme-linked secondary antibody is then added to the solid phase
to determine the amount of primary antibody bound to the solid
phase.
[0175] In an "immunohistochemistry assay" a section of tissue is
tested for specific proteins by exposing the tissue to antibodies
that are specific for the protein that is being assayed. The
antibodies are then visualized by any of a number of methods to
determine the presence and amount of the protein present. Examples
of methods used to visualize antibodies are, for example, through
enzymes linked to the antibodies (e. g., luciferase, alkaline
phosphatase, horseradish peroxidase, or P-galactosidase), or
chemical methods (e.g., DAB/Substrate chromagen) or gold,
fluorescent or labelled antibodies by any of the many different
methods known to those skilled in this art.
Measure at the Nucleic Level
[0176] In another embodiment of the method of prediction of the
risk that a chemotherapeutic anti-cancer treatment induces cancer
stem cells according to the invention, the expression levels of
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform in said
untreated and treated cancer sample are measured at the nucleic
level by measuring the amount of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms mRNA or corresponding cDNA. In this
case, preliminary substeps of transformation of the untreated and
treated cancer sample may include a substep of extraction of mRNAs
present in the cancer sample, optionally followed by converting
said mRNAs into cDNA. Methods for extracting mRNAs from a cell or
tissue sample and for converting mRNAs into cDNAs are well known to
those skilled in the art. Such preliminary substep of extracting
mRNAs and optionally of converting mRNAS into cDNAs are
nevertheless not necessary when some particular technologies able
to measure the amount of a particular mRNA directly in a cell or
tissue sample are used (such as in situ hybridization).
[0177] When the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in said untreated and treated cancer
sample is measured at the nucleic level by measuring the amount of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms mRNA or
corresponding cDNA, any appropriate technology known to those
skilled in the art for measuring mRNA or cDNA expression levels may
be used. Suitable technologies include nucleic microarrays,
quantitative PCR, next generation sequencing and hybridization with
a labelled probe (including Northern hybridization and in situ
hybridization).
[0178] In particular, real time quantitative RT-PCR (qRT-PCR) may
be useful. qRT-PCR is a well-known and easily available technology
for those skilled in the art and does not need a precise
description. Examples of qRT-PCR-based methods can be found, for
example, in U.S. Pat. No. 7,101,663. Commercially available qRT-PCR
based methods (e.g., Taqman.RTM. Array) may for instance be
employed, the design of primers and/or probe being easily made
based on the sequences of .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform disclosed in Table 1 above. In a
preferred embodiment of the method of prediction of the invention,
the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in said cancer sample is measured at
the nucleic level by measuring the amount of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms mRNA or corresponding cDNA by
qRT-PCR.
[0179] Nucleic acid assays or arrays can also be used to assess in
vitro the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in a cancer sample, by measuring in
vitro the amount of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms mRNA or cDNA in the cancer sample. In
some embodiments, a nucleic acid microarray can be prepared or
purchased. An array typically contains a solid support and at least
one nucleic acid (cDNA or oligonucleotide) contacting the support,
where the oligonucleotide corresponds to at least a portion of a
gene. Any suitable assay platform can be used to measure in vitro
the amount of .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
in a cancer sample. For example, an assay may be in the form of a
membrane, a chip, a disk, a test strip, a filter, a microsphere, a
multiwell plate, and the like. An assay system may have a solid
support on which a nucleic acid (cDNA or oligonucleotide) binding
to the .DELTA.133p53.beta. isoform, the .DELTA.133p53.gamma.
isoform, or both the 133p536 and .DELTA.133p53.gamma. isoforms mRNA
or cDNA is attached. The solid support may comprise, for example, a
plastic, silicon, a metal, a resin, or a glass. The assay
components can be prepared and packaged together as a kit for
detecting a gene. To determine the expression profile of a target
nucleic sample, said sample is labelled, contacted with the
microarray in hybridization conditions, leading to the formation of
complexes between target nucleic acids that are complementary to
probe sequences attached to the microarray surface. The presence of
labelled hybridized complexes is then detected. Many variants of
the microarray hybridization technology are available to the person
skilled in the art.
[0180] Other technologies using hybridization with a labelled probe
may be used. The sequence of the labelled probe will be selected to
specifically hybridize under stringent conditions to the
.DELTA.133p53.beta. isoform, the .DELTA.133p53.gamma. isoform, or
both the .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms mRNA
or cDNA. Examples of suitable probes sequences are disclosed in
Table 4 below. The labelled probe includes a label group attached
thereto, e. g., a radioisotope, a fluorescent compound, an enzyme,
or an enzyme co-factor.
[0181] In another embodiment, the in vitro measure of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms mRNA or cDNA
expression level may be performed by sequencing mRNA or cDNA
extracted from the cancer sample.
[0182] In some embodiments, the mRNA or cDNA sample may be
amplified to increase the sensitivity of detection of the method.
Such amplification may be performed using any suitable technology
known to those skilled in the art, including PCR or RT-PCR
reaction. In this case, primers permitting amplification of the
.DELTA.133p53.beta. isoform, the .DELTA.133p53.gamma. isoform, or
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms mRNA or
cDNA are used. Said primers may notably have the sequences
presented in Table 4 below.
TABLE-US-00005 TABLE 4 Examples of suitable forward/reward
amplification primers and hybridization probes for amplifying or
detecting .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms. B isoforms (p53 TAB, .DELTA.133p53 isoforms
.DELTA.40p53.beta., .DELTA.133p53.beta., (.alpha., .beta. and
.gamma.) and .DELTA.160p53.beta.) Forward 5'-ACTCTGTCTCCTTCC
5'-AACCACTGGATGGAGAA primer TCTTCCTACAG-3' TATTTCAC-3' (SEQ ID NO:
7) (SEQ ID NO: 10) Reward 5'-GTGTGGAATCAACCC 5'-TCATAGAACCACATG
primer ACAGCT-3' CTCTCTT-3' (SEQ ID NO: 8) (SEQ ID NO: 11) Hybridi-
5'-TCCCCTGCCCTCA 5'-CAGGACCAGACCAGCTT zation ACAAGATGTTTTGCC-3'
TCAAAAAGAAAATTGTT-3' probe (SEQ ID NO: 9) (SEQ ID NO: 12)
Step b)--Treatment of the Cancer Sample with Said Chemotherapeutic
Anti-Cancer Agent
[0183] In step b), the cancer sample (or part thereof) is treated
with said chemotherapeutic anti-cancer agent.
Step d) Comparison of the Expression Levels Measured in Steps a)
and c)
[0184] In step d), the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms in the subject's treated cancer
sample measured in step c) is compared to the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in the
subject's untreated cancer sample measured in step a).
[0185] More particularly, it is determined if the expression level
of .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in the
subject's treated cancer sample measured in step c) is: [0186] (i)
Higher than the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in the subject's untreated cancer
sample measured in step a), or [0187] (ii) Lower than or equal to
the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in the subject's untreated cancer
sample measured in step a). Step e)--Prediction of the Risk of
Induction of Cancer Stem Cells)
[0188] In step e), it is concluded to: [0189] (i) the presence of a
significant risk that treatment with said chemotherapeutic
anti-cancer agent induces cancer stem cells in said subject if the
expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms measured in step c) is higher than
the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms measured in step a), or [0190] (ii)
the absence of a significant risk that treatment with said
chemotherapeutic anti-cancer agent induces cancer stem cells in
said subject if the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms measured in step c) is lower than
or equal to the expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms measured in step a).
Preferred Embodiments
[0191] Various preferred specific features corresponding to various
generic elements of the method for predicting the risk that
treatment with a chemotherapeutic anti-cancer agent induces cancer
stem cells in a subject suffering from cancer according to the
invention have been described above in the section specifically
relating to this element. In the context of the invention, each
list of appropriate features for a particular element and each
specific feature disclosed for a particular element may be combined
with any generic other element, list of appropriate features for
said other element or any specific feature disclosed for said other
element.
[0192] In particular, preferred embodiments of an element of the
method for predicting the risk that treatment with a
chemotherapeutic anti-cancer agent induces cancer stem cells in a
subject suffering from cancer according to the invention may be
combined with any generic other element or with preferred
embodiments of said other element. Preferred embodiments correspond
to those in which at least one element is limited to a preferred
embodiment, as listed in Table 5 below:
TABLE-US-00006 TABLE 5 Preferred embodiment of various elements of
the method for predicting the risk that treatment with a
chemotherapeutic anti-cancer agent induces cancer stem cells in a
subject suffering from cancer according to the invention. Element
Preferred embodiment(s) Cancer cell Breast cancer cell or
colorectal cancer Chemotherapeutic anti-cancer topoisomerase II
inhibitor, preferably agent etoposide P53 isoform which expression
is .DELTA.133p53.beta. isoform or .DELTA.133p53.beta. and measured
in steps a) and c) .DELTA.133p53.gamma. isoforms, preferably
.DELTA.133p53.beta. isoform Method for measuring expression Nucleic
acid level, preferably by level q-RT-PCR
[0193] In a particularly preferred embodiment of the method for
predicting the risk that treatment with a chemotherapeutic
anti-cancer agent induces cancer stem cells in a subject suffering
from cancer according to the invention, cancer cells provided in
step a) are breast cancer cells, the P53 isoform which expression
is measured in steps a) and c) is .DELTA.133p53.beta. isoform or
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms, and the
expression level is measured at the nucleic level by measuring the
amount of mRNA or corresponding cDNA.
Treatment of Cancer in a Subject Suffering from a Cancer
[0194] Based on the same finding of the inventors that anticancer
treatment of cancer cells by etoposide (a topoisomerase II
inhibitor) may not be only inefficient (resistance to treatment)
but may further promote cancer sternness by increasing
.DELTA.133p53.beta. expression level, the present invention also
relates to a chemotherapeutic anti-cancer agent, for use in the
treatment of cancer in a subject suffering from a cancer, wherein
said chemotherapeutic anti-cancer agent is administered to said
subject in combination with an agent reducing .DELTA.133p53.beta.
or .DELTA.133p53.gamma. isoform expression.
[0195] Similarly, the present invention also relates to a method
for treating cancer in a subject suffering from a cancer,
comprising:
a) Administering to said subject a therapeutically efficient amount
of an agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression; and b) Administering to
said subject a therapeutically efficient amount of a
chemotherapeutic anti-cancer treatment.
Chemotherapeutic Anti-Cancer Treatment
[0196] In the therapeutic uses according to the invention, the
chemotherapeutic anti-cancer agent administered to a cancer subject
may be any one of those listed by the American Cancer Society.
Preferably the chemotherapeutic anti-cancer agent is selected from:
[0197] a topoisomerase II inhibitor, including etoposide,
etoposide, tenoposide, doxorubicine, daunorubicin, mitoxantrone,
and amsacrine; [0198] an anti-tubuline agent, including taxanes
such as paclitaxel and docetaxel, and vinca alkaloids such as
vinblastine, vincristine, vindesine, and vinorelbine; [0199]
antimetabolites, including pyrimidine analogue 5-Fluorouracil
(5-FU).
[0200] In a preferred embodiment, the chemotherapeutic anti-cancer
treatment administered to a cancer subject is a topoisomerase II
inhibitor, in particular selected from etoposide, etoposide,
tenoposide, doxorubicine, daunorubicin, mitoxantrone, and
amsacrine. More preferably, the chemotherapeutic anti-cancer
treatment administered to a cancer subject is etoposide.
Agent Reducing .DELTA.133p538 Isoform, .DELTA.133p53.gamma.
Isoform, or Both .DELTA.133p538 and .DELTA.133p53.gamma. Isoforms
Expression
[0201] Any agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression may be used.
[0202] Agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression include antisense RNA or
interfering RNA (iRNA), including more particularly small
interfering RNAs (siRNAs) and short hairpin RNAS (shRNAs).
[0203] Sequences targeted by specific shRNAs reducing
.DELTA.133p53.beta. and/or .DELTA.133p53.gamma. isoform expression
are provided in Table 6 below:
TABLE-US-00007 TABLE 6 Sequences targeted by specific shRNAs
reducing .DELTA.133p53.beta. and/or .DELTA.133p53.gamma. isoform
expression. Region of p53 targeted/ Name targeted isoforms 5' to 3'
sequence Sh1 DBD domain/all p53 5'-GACTCCAGTGGTAATCTA isoforms C-3'
(SEQ ID NO: 13) Sh3 5' UTR of .DELTA.133 isoforms/
5'-GGAGGTGCTTACACATGT all .DELTA.133 isoforms T-3' (SEQ ID NO: 14)
(.alpha., .beta. and .gamma.) Sh4 5' UTR of .DELTA.133 isoforms/
5'-CTTGTGCCCTGACTTTCA all .DELTA.133 isoforms A-3' (SEQ ID NO: 15)
(.alpha., .beta. and .gamma.) Sh5 3'end of B isoforms
5'-GGACCAGACCAGCTTTC (p53 TAB, .DELTA.40p53.beta., A-3' (SEQ ID NO:
16) .DELTA.133p53.beta., and .DELTA.160p53.beta.)
[0204] .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms are
expressed when alternative splicing of p53 gene occurs. As a
result, agents reducing .DELTA.133p53.beta. and/or
.DELTA.133p53.gamma. isoform expression also include agents
targeting alternative splicing, including compounds of formulas
(I), (Ia), (Ib), (Ic), (Id), (Ie), (If), (Ig), (Ih), (Ii), (Ij),
(Ik), (Il), (Im, (Io), (Ip), (Iq), (Ir), (Iee), and more
particularly compounds (1) to (168) and pharmaceutically acceptable
salts thereof disclosed in WO2010/143168. Compounds (6), (18),
(30), (35), (36), (37), (45), (48), (51), (52), (53), (55), (56),
(58), (61), (63), (64), (109), (110), (112), (143), (144) and (148)
are preferred.
[0205] The skilled artisan will be able to screen other agents
reducing .DELTA.133p53.beta. and/or .DELTA.133p53.gamma. isoform
expression by using the screening method of the present
invention.
Administration Regimen
[0206] The chemotherapeutic anti-cancer agent and the agent
reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
expression are administered in therapeutically efficient
amounts.
[0207] The chemotherapeutic anti-cancer agent and the agent
reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
expression may be administered simultaneously (in a same
composition or in two distinct compositions) or sequentially, or
both simultaneously (in a same composition or in two distinct
compositions) and sequentially (i.e. both compounds are
administered simultaneously during a period, but one or the other
compound is administered alone before and/or after the simultaneous
administration period).
[0208] In an embodiment, both compounds are administered
simultaneously (in a same composition or in two distinct
compositions).
[0209] In another embodiment, both compounds are administered
sequentially. In this case, the chemotherapeutic anti-cancer agent
may be administered before the agent reducing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms expression, or the agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
may be administered before the chemotherapeutic anti-cancer
agent.
[0210] In another embodiment, both compounds are administered
simultaneously during a period, but one or the other compound is
administered alone before and/or after the simultaneous
administration period. This includes: [0211] Prior administration
of chemotherapeutic anti-cancer agent alone followed by
simultaneous administration of chemotherapeutic anti-cancer agent
and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, [0212] Prior
administration of agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression alone followed by
simultaneous administration of chemotherapeutic anti-cancer agent
and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, [0213] Simultaneous
administration of chemotherapeutic anti-cancer agent and agent
reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
expression followed by administration of chemotherapeutic
anti-cancer agent alone, [0214] Simultaneous administration of
chemotherapeutic anti-cancer agent and agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
followed by administration of agent reducing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms expression alone, [0215] Prior
administration of chemotherapeutic anti-cancer agent alone followed
by simultaneous administration of chemotherapeutic anti-cancer
agent and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, followed by
administration of chemotherapeutic anti-cancer agent alone, [0216]
Prior administration of chemotherapeutic anti-cancer agent alone
followed by simultaneous administration of chemotherapeutic
anti-cancer agent and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, followed by
administration of agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression alone, [0217] Prior
administration of agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression alone followed by
simultaneous administration of chemotherapeutic anti-cancer agent
and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, followed by
administration of chemotherapeutic anti-cancer agent alone, and
[0218] Prior administration of agent reducing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms expression alone followed by
simultaneous administration of chemotherapeutic anti-cancer agent
and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, followed by
administration of agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression alone.
[0219] Since chemotherapeutic anti-cancer agent may promote
induction of cancer stem cells, preferred administration regimens
are those in which the agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression is administered
simultaneously (at least during a period, in a same composition or
in two distinct compositions) and/or after administration of the
chemotherapeutic anti-cancer agent. Such preferred administration
regimens include: [0220] Simultaneous administration of both
compounds, [0221] Chemotherapeutic anti-cancer agent administration
alone followed by administration of agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
alone, [0222] Simultaneous administration of chemotherapeutic
anti-cancer agent and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression followed by administration
of agent reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms expression alone, [0223] Prior administration of
chemotherapeutic anti-cancer agent alone followed by simultaneous
administration of chemotherapeutic anti-cancer agent and agent
reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform,
or both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
expression, followed by administration of agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
alone, and [0224] Prior administration of agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
alone followed by simultaneous administration of chemotherapeutic
anti-cancer agent and agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression, followed by
administration of agent reducing .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms expression alone.
Preferred Embodiments
[0225] Various preferred specific features corresponding to various
generic elements of the therapeutic uses of a combination of a
chemotherapeutic anti-cancer agent and an agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
according to the invention have been described above in the section
specifically relating to this element. In the context of the
invention, each list of appropriate features for a particular
element and each specific feature disclosed for a particular
element may be combined with any generic other element, list of
appropriate features for said other element or any specific feature
disclosed for said other element. In particular, preferred
embodiments of an element of the therapeutic uses of a combination
of a chemotherapeutic anti-cancer agent and an agent reducing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms expression
according to the invention may be combined with any generic other
element or with preferred embodiments of said other element.
[0226] Preferred embodiments correspond to those in which at least
one element is limited to a preferred embodiment, as listed in
Table 7 below:
TABLE-US-00008 TABLE 7 Preferred embodiment of various elements of
the therapeutic uses of a combination of a chemotherapeutic
anti-cancer agent and an agent reducing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms expression according to the
invention. Element Preferred embodiment(s) Cancer Breast cancer or
colorectal cancer Chemotherapeutic anti-cancer topoisomerase II
inhibitor, preferably agent etoposide agent reducing
.DELTA.133p53.beta. siRNA, shRNAs, or agents targeting isoform,
.DELTA.133p53.gamma. isoform, or alternative splicing both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms
Administration regimen the agent reducing .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms expression is administered
simultaneously (at least during a period, in a same composition or
in two distinct compositions) and/or after administration of the
chemotherapeutic anti-cancer agent
[0227] In a particularly preferred embodiment of the therapeutic
uses of a combination of a chemotherapeutic anti-cancer agent and
an agent reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms expression according to the invention, cancer is breast
cancer, the chemotherapeutic anti-cancer agent is etoposide, the
agent reducing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms is a siRNA, a shRNA or an agent targeting alternative
splicing selected from compounds of formulas (I), (Ia), (Ib), (Ic),
(Id), (Ie), (If), (Ig), (Ih), (Ii), (Ij), (Ik), (Il), (Im, (Io),
(Ip), (Iq), (Ir), (Iee), and more particularly compounds (1) to
(168) and pharmaceutically acceptable salts thereof disclosed in
WO2010/143168 (in particular compounds (6), (18), (30), (35), (36),
(37), (45), (48), (51), (52), (53), (55), (56), (58), (61), (63),
(64), (109), (110), (112), (143), (144) and (148)).
Prediction of Risk of Metastasis
[0228] The results obtained by the inventors show that
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform expression
promotes cancer stem cell potential, in particular by upregulating
expression of transcription factors Sox 2, Oct 3/4 and Nanog,
suggesting that expression of .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform may be an early event of reprogramming
of cancer cells towards cancer stem cells, and that detection of
other cancer stem cells features in addition to detection of
.DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform expression may
improve the reliability of prediction of a risk of cancer
metastasis in a subject suffering from cancer. The present
invention thus also relates to a method for predicting a risk of
cancer metastasis in a subject suffering from cancer from a cancer
sample of said subject, comprising:
a) detecting sphere-forming cancer cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in said
cancer sample; and b) concluding to the presence of a significant
risk of cancer metastasis in said subject if sphere-forming cancer
cells expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are detected and to the absence of a significant risk of
cancer metastasis in said subject if sphere-forming cancer cells
expressing .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms are not detected.
Cancer and Cancer Sample
[0229] In the method of prediction of risk of metastasis according
to the invention, the cancer from which the subject is suffering is
preferably selected from the group of solid cancers, and in
particular from the group consisting of breast cancer, ovarian
cancer, digestive cancers (also referred as gastrointestinal
cancer, including colorectal cancer oesophageal cancer, gastric
cancer, pancreatic cancer, hepatocellular carcinoma,
cholangiocellular cancer and teratocarcinoma), pancreatic cancer
and throat cancer, particularly of human subject, more preferably
from breast cancer, colorectal cancer gastrointestinal cancer, lung
cancer and prostate cancer, and even more preferably the cancer
from which the subject is suffering is breast cancer or colorectal
cancer. Moreover, the cancer from which the subject is suffering
may be selected from the group of hematopoietic cancers, and in in
particular from the group consisting of leukaemias and lymphomas.
Preferably, the hematopoietic cancer is a human hematopoietic
cancer.
[0230] It is known in the art that many types of cancer cells, when
transduced by at least one and preferably several of Yamanaka
factors (Oct 3/4, Nanog, Sox 2 and c-Myc), may give rise to CSCs.
Examples of cancer cells in which this has been shown include:
[0231] colon (or colorectal) cancer cells (see for instance Oshima
et al (2014), which describes that colon cancer cells transduced
with factors Oct 3/4, Sox 2 and KLF4 showed significantly enhanced
CSCs proprieties in terms of marker gene expression and sphere
formation), [0232] gastrointestinal cancer cells (including cells
of colorectal cancer, oesophageal cancer, gastric cancer,
pancreatic cancer, hepatocellular carcinoma, cholangiocellular
cancer and teratocarcinoma). Miyoshi et al (2010) disclose that
cells obtained from the above cited gastrointestinal cancers
induced with Nanog transcriptional factor manifest a pluripotency
like CSCs, [0233] lung cancer cells (see Chiou et al., 2010, which
describes that ectopic expression of Oct4 and Nanog transcriptional
factors in lung adenocarcinoma cells induce the sphere formation),
and [0234] prostate cancer cells (see Jeter et al, 2011, which
describes that tetracycline-inducible Nanog-overexpression in
prostate cancer cell lines promotes tumour regeneration by
enhancing the expression of several CSCs associated molecules.
[0235] Since transduction with .DELTA.133p53.beta. isoform or
.DELTA.133p53.gamma. isoform induces the expression of Sox 2, Nanog
and Oct 3/4, its transduction in any cancer cell known to give rise
to CSCs when transduced by at least one and preferably several of
Yamanaka factors (Oct 3/4, Nanog, Sox 2 and c-Myc) is expected to
generate CSCs. This has been demonstrated by the inventors for two
distinct types of cancer cells: breast and colon cancer cells.
[0236] The cancer sample from which the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is measured
in step a) may be a cancer biopsy or a complete or partial cancer
surgical resection. Alternatively, the cancer sample from which the
expression level of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is measured in step a) may be a blood
sample. Indeed, cancer cells (including cancer stem cells) are well
known to circulate in blood (Mavroudis-2010; Alix-Panabieres et
al., 2013)
Isoform
[0237] In a preferred embodiment of the method of risk of
metastasis according to the invention, it is the expression level
of .DELTA.133p53.beta. isoform or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms that is measured in step a). Indeed,
expression of .DELTA.133p53.beta. isoform is particularly
associated to induction of cancer stem cells.
Detection of 4133p538 Isoform, 4133p53.gamma. Isoform, or Both
4133p538 and .DELTA.133p53.gamma. Isoforms Expression
[0238] In step a), expression of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is detected.
[0239] For this purpose, any method disclosed in relation to the
method of prediction of the risk that a chemotherapeutic
anti-cancer treatment induces cancer stem cells according to the
invention may be used.
Detection of Cancer Cells Sphere-Forming Capacity
[0240] The cancer stem cell phenotype is also characterized by the
preferential ability of cancer stem cells to form spheres under
serum-free (and preferably low adherence) culture conditions,
whereas bulk tumor cells are less likely to be able to form spheres
under the same conditions.
[0241] The sphere-forming capacity of cancer cells may be tested
using an assay comprising: [0242] i) resuspending cancer cells into
a serum-free medium, preferably in the presence of specific growth
factors (including, but not limited to, Epidermal Growth Factor
(EGF) and basic Fibroblast Growth Factor (bFGF)), and plating them
into tissue culture dishes, to which mammalian cells preferably
poorly adhere; [0243] ii) incubating the cancer cells during 5 to
20 days; and [0244] iii) counting spheres.
[0245] In step i), cancer cells are resuspended into a serum-free
medium (e.g., MammoCult.RTM., available from StemCell Technologies,
Inc., Vancouver, Canada), preferably in the presence of specific
growth factors such as EGF and bFGF, and plated into tissue culture
dishes. Preferably, tissue culture dishes to which mammalian cells
poorly adhere are selected (e.g. Ultra Low Cluster Plate, 24-well,
Flat Bottom from Corning Inc). In this step, the seeding density is
preferably kept between 250 and 2500 cells/cm.sup.2, and is
preferably optimized for each type of cancer cells.
[0246] For instance, for breast cancer cells in MammoCult.TM.
Medium enriched with MammoCult.TM. Proliferation Supplements,
hydrocortisone and heparin (Stem Cell Technologies), a seeding
density of 500 cells/well of Ultra Low Cluster Plate, 24-well, Flat
Bottom (Corning Inc) is appropriate.
[0247] In step ii), cancer cells are incubated, preferably at about
37.degree. C. under 5% CO.sub.2 atmosphere, during 5 to 20 days,
preferably during 7 to 15 days.
[0248] Finally, in step c), spheres that have formed during
incubation are counted. Such counting is preferably made using a
microscope, preferably a phase-contrast microscope, and spheres
that are at least 50 .mu.m large are preferably counted.
[0249] It is considered that a cancer sample contains
sphere-forming cancer cells when spheres can be counted at least at
the maximal seeding density of 2500 cells/cm.sup.2.
Preferred Embodiments
[0250] Various preferred specific features corresponding to various
generic elements of the method for predicting risk of metastasis
according to the invention have been described above in the section
specifically relating to this element. In the context of the
invention, each list of appropriate features for a particular
element and each specific feature disclosed for a particular
element may be combined with any generic other element, list of
appropriate features for said other element or any specific feature
disclosed for said other element.
[0251] In particular, preferred embodiments of an element of the
method for predicting risk of metastasis according to the invention
may be combined with any generic other element or with preferred
embodiments of said other element.
[0252] Preferred embodiments correspond to those in which at least
one element is limited to a preferred embodiment, as listed in
Table 8 below:
TABLE-US-00009 TABLE 8 Preferred embodiment of various elements of
the method for predicting risk of metastasis according to the
invention. Element Preferred embodiment(s) Cancer Breast cancer or
colorectal cancer P53 isoform which expression is
.DELTA.133p53.beta. isoform or .DELTA.133p53.beta. and detected in
step a) .DELTA.133p53.gamma. isoforms, preferably
.DELTA.133p53.beta. isoform Method for detecting P53 isoform
Nucleic acid level, preferably by expression q-RT-PCR Method for
detecting sphere- An assay comprising: forming ability i)
resuspending cancer cells into a serum-free medium, preferably in
the presence of specific growth factors such as EGF and bFGF, and
plating them into tissue culture dishes, to which mammalian cells
poorly adhere, at a seeding density between 250 and 2500
cells/cm.sup.2; ii) incubating the cancer cells during 7 to 15
days; and iii) counting spheres that are at least 50 .mu.m
large.
[0253] In a particularly preferred embodiment of the method for
predicting risk of metastasis according to the invention, cancer is
breast cancer, the P53 isoform which expression is detected in step
a) is .DELTA.133p53.beta. isoform or .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms, its/their the expression level(s)
is/are measured at the nucleic level by measuring the amount of
mRNA or corresponding cDNA (preferably by q-RT-PCR), and
sphere-forming ability is detected by the preferred assay described
in Table 8 above.
Prediction of Risk of Cancer Relapse in a Treated Cancer
Patient
[0254] As mentioned above, the results obtained by the inventors
show that .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
expression promotes cancer stem cell potential, in particular by
upregulating expression of transcription factors Sox 2, Oct 3/4 and
Nanog, suggesting that expression of .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform may be an early event of reprogramming
of cancer cells towards cancer stem cells. It is thus possible to
predict if a treated cancer subject, in which most cancer cells
have been successfully eliminated, is risking cancer relapse if one
or both of .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoforms
is/are expressed in a cell sample obtained from said subject.
[0255] The present invention thus also relates to a method for
predicting a risk of cancer relapse in a treated cancer subject
from a cell sample of said subject, comprising:
a) detecting the expression of .DELTA.133p53.beta. isoform, of
.DELTA.133p53.gamma. isoform, or of both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in said cell sample; and b)
concluding to the presence of a significant risk of cancer relapse
in said subject if the expression of .DELTA.133p53.beta. isoform,
of .DELTA.133p53.gamma. isoform, or of both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is detected and to the absence of a
significant risk of cancer relapse in said subject if neither the
expression of .DELTA.133p53.beta. isoform nor the expression of
.DELTA.133p53.gamma. isoform are detected.
[0256] Optionally, the method for predicting a risk of cancer
relapse in a treated cancer subject according to the invention may
also comprise an additional step c) of comparing the expression of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or of
both .DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms in the
tested cell sample to expression of the same isoforms in a
previously tested cancer sample from said treated cancer
subject.
[0257] This method may be performed in one or several ways after
the treatment of cancer as a preventive method in order to confirm
diagnosis of cancer relapse.
Cancer and Non-Cancerous Cell Sample
[0258] In the method of prediction of risk of cancer relapse
according to the invention, the cancer for which the subject has
been successfully treated (most of cancer cells have been
eliminated) is preferably selected from the group of solid cancers,
and in particular from the group consisting of breast cancer,
ovarian cancer, digestive cancers (also referred as
gastrointestinal cancer, including colorectal cancer oesophageal
cancer, gastric cancer, pancreatic cancer, hepatocellular
carcinoma, cholangiocellular cancer and teratocarcinoma),
pancreatic cancer and throat cancer, particularly of human subject,
more preferably breast cancer colorectal cancer, gastrointestinal
cancer, lung cancer and prostate cancer and even more preferably
the cancer is breast cancer or colorectal cancer.
[0259] Moreover, the cancer may be selected from the group of
hematopoietic cancers, and in particular from the group consisting
of leukaemias and lymphomas. Preferably, the hematopoietic cancer
is a human hematopoietic cancer.
[0260] It is known in the art that many types of cancer cells, when
transduced by at least one and preferably several of Yamanaka
factors (Oct 3/4, Nanog, Sox 2 and c-Myc), may give rise to CSCs.
Examples of cancer cells in which this has been shown include:
[0261] colon (or colorectal) cancer cells (see for instance Oshima
et al (2014), which describes that colon cancer cells transduced
with factors Oct 3/4, Sox 2 and KLF4 showed significantly enhanced
CSCs proprieties in terms of marker gene expression and sphere
formation), [0262] gastrointestinal cancer cells (including cells
of colorectal cancer, oesophageal cancer, gastric cancer,
pancreatic cancer, hepatocellular carcinoma, cholangiocellular
cancer and teratocarcinoma). Miyoshi et al (2010) disclose that
cells obtained from the above cited gastrointestinal cancers
induced with Nanog transcriptional factor manifest a pluripotency
like CSCs, [0263] lung cancer cells (see Chiou et al., 2010, which
describes that ectopic expression of Oct4 and Nanog transcriptional
factors in lung adenocarcinoma cells induce the sphere formation),
and [0264] prostate cancer cells (see Jeter et al, 2011, which
describes that tetracycline-inducible Nanog-overexpression in
prostate cancer cell lines promotes tumour regeneration by
enhancing the expression of several CSCs associated molecules.
[0265] Since transduction with .DELTA.133p53.beta. isoform or
.DELTA.133p53.gamma. isoform induces the expression of Sox 2, Nanog
and Oct 3/4, its transduction in any cancer cell known to give rise
to CSCs when transduced by at least one and preferably several of
Yamanaka factors (Oct 3/4, Nanog, Sox 2 and c-Myc) is expected to
generate CSCs. This has been demonstrated by the inventors for two
distinct types of cancer cells: breast and colon cancer cells.
[0266] The cell sample from which the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is measured
in step a) may be a biopsy of a tissue previously affected by a
cancer of those described above or of subjacent tissue.
Alternatively, the cancer sample from which the expression level of
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms is measured
in step a) may be a blood sample. Indeed, cancer cells (including
cancer stem cells) are well known to circulate in blood
(Mavroudis-2010; Alix-Panabieres et al., 2013)
Isoform
[0267] In a preferred embodiment of the method of risk of relapsing
cancer according to the invention, it is the expression level of
.DELTA.133p53.beta. isoform or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms that is measured in step a). Indeed,
expression of .DELTA.133p53.beta. isoform is particularly
associated to induction of cancer stem cells.
Detection of .DELTA.133p538 Isoform, .DELTA.133p53.gamma. Isoform,
or Both .DELTA.133p538 and .DELTA.133p53.gamma. Isoforms
Expression
[0268] In step a), expression of .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms is detected.
[0269] For this purpose, any method disclosed in relation to the
method of prediction of the risk that a chemotherapeutic
anti-cancer treatment induces cancer stem cells according to the
invention may be used.
Preferred Embodiments
[0270] Various preferred specific features corresponding to various
generic elements of the method for predicting risk of metastasis
according to the invention have been described above in the section
specifically relating to this element. In the context of the
invention, each list of appropriate features for a particular
element and each specific feature disclosed for a particular
element may be combined with any generic other element, list of
appropriate features for said other element or any specific feature
disclosed for said other element.
[0271] In particular, preferred embodiments of an element of the
method for predicting risk of relapsing of cancer of cured patient
according to the invention may be combined with any generic other
element or with preferred embodiments of said other element.
Preferred embodiments correspond to those in which at least one
element is limited to a preferred embodiment, as listed in Table 8a
below:
TABLE-US-00010 TABLE 8a Preferred embodiment of various elements of
the method for predicting risk of relapsing of cancer cured subject
according to the invention. Element Preferred embodiment(s) Cancer
Breast cancer or colorectal cancer P53 isoform which expression is
.DELTA.133p53.beta. isoform or .DELTA.133p53.beta. and detected in
step a) .DELTA.133p53.gamma. isoforms, preferably
.DELTA.133p53.beta. isoform Method for detecting P53 isoform
Nucleic acid level, preferably by expression q-RT-PCR Cell sample
Tissue sample
[0272] In a particularly preferred embodiment of the method for
predicting risk of relapsing of a cancer cured subject according to
the invention, cancer is breast cancer, the P53 isoform which
expression is detected in step a) is .DELTA.133p53.beta. isoform or
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms, its/their
the expression level(s) is/are measured at the nucleic level by
measuring the amount of mRNA or corresponding cDNA (preferably by
q-RT-PCR) in the non-cancerous cell tissue sample.
Screening of Anti-Cancer Stem Cells Agents
[0273] Based on the same finding that .DELTA.133p53.beta. or
.DELTA.133p53.gamma. isoform expression promotes cancer stem cell
potential, in particular by upregulating expression of
transcription factors Sox 2, Oct 3/4 and Nanog, suggesting that
expression of .DELTA.133p53.beta. or .DELTA.133p53.gamma. isoform
may be an early event of reprogramming of cancer cells towards
cancer stem cells, the present invention also relates to a method
for screening potential anti-cancer stem cells compounds,
comprising:
a) providing sphere-forming cancer stem cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms; b)
contacting said cancer stem cells with a test compound; c)
measuring in vitro the expression level of said .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms in treated cells and/or the
sphere-forming ability of treated cells; d) selecting said test
compound as a potential anti-cancer stem cells compound if the
expression level of said .DELTA.133p53.beta. isoform,
.DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms in treated cells is lower than before
treatment with the test compound, and/or if the sphere-forming
ability of treated cells is lower than before treatment with the
test compound. Sphere-Forming Cancer Stem Cells Expressing
.DELTA.133p538 Isoform, .DELTA.133p53.gamma. Isoform, or Both
.DELTA.133p538 and .DELTA.133p53.gamma. Isoforms
[0274] Sphere-forming cancer stem cells expressing
.DELTA.133p53.beta. isoform, .DELTA.133p53.gamma. isoform, or both
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms provided in
step a) may be either purified from a cancer sample or produced
according to the method for producing cancer stem cells according
to the invention.
[0275] When purified from a cancer sample, they may be obtained by
submitting bulk cancer cells of the cancer sample to a
sphere-forming assay, recovering spheres obtained in the assay and
checking for .DELTA.133p53.beta. isoform, .DELTA.133p53.gamma.
isoform, or both .DELTA.133p53.beta. and .DELTA.133p53.gamma.
isoforms expression.
Test Compounds
[0276] The type of compounds tested in the method for screening of
anti-cancer stem cells agents according to the invention are not
particularly limited, and any type of chemical or biological
compound may be tested.
[0277] Examples of test compounds include siRNAs, shRNAs, and
agents targeting alternative splicing.
Measure of the Expression Level of Said .DELTA.133p538 Isoform,
.DELTA.133p53.gamma. Isoform, or Both .DELTA.133p538 and
.DELTA.133p53.gamma. Isoforms
[0278] In step c), the expression level of .DELTA.133p53.beta.
isoform, .DELTA.133p53.gamma. isoform, or both .DELTA.133p53.beta.
and .DELTA.133p53.gamma. isoforms may be measured in vitro.
[0279] For this purpose, any method disclosed in relation to the
method of prediction of the risk that a chemotherapeutic
anti-cancer treatment induces cancer stem cells according to the
invention may be used.
Measure of Sphere-Forming Ability of Treated Cells
[0280] In step c), the sphere-forming ability of treated cells may
be measured in vitro.
[0281] For this purpose, the assay disclosed above in relation of a
method for predicting risk of metastasis according to the invention
is preferably used.
Preferred Embodiments
[0282] Various preferred specific features corresponding to various
generic elements of the method of screening of anti-cancer stem
cells agents according to the invention have been described above
in the section specifically relating to this element. In the
context of the invention, each list of appropriate features for a
particular element and each specific feature disclosed for a
particular element may be combined with any generic other element,
list of appropriate features for said other element or any specific
feature disclosed for said other element.
[0283] In particular, preferred embodiments of an element of the
method of screening of anti-cancer stem cells agents according to
the invention may be combined with any generic other element or
with preferred embodiments of said other element.
[0284] Preferred embodiments correspond to those in which at least
one element is limited to a preferred embodiment, as listed in
Table 9 below:
TABLE-US-00011 TABLE 9 Preferred embodiment of various elements of
the method of screening of anti- cancer stem cells agents according
to the invention. Element Preferred embodiment(s) Cancer Breast
cancer or colorectal cancer P53 isoform which expression is
.DELTA.133p53.beta. isoform or .DELTA.133p53.beta. detected in step
a) and .DELTA.133p53.gamma. isoforms, preferably
.DELTA.133p53.beta. isoform Method for detecting P53 isoform
Nucleic acid level, preferably by expression q-RT-PCR Method for
detecting sphere- An assay comprising: forming ability i)
resuspending cancer cells into a serum-free medium, preferably in
the presence of specific growth factors such as EGF and bFGF, and
plating them into tissue culture dishes, to which mammalian cells
poorly adhere, at a seeding density between 250 and 2500
cells/cm.sup.2; ii) incubating the cancer cells during 7 to 15
days; and iii) counting spheres that are at least 50 .mu.m
large.
[0285] In a particularly preferred embodiment of the method of
screening of anti-cancer stem cells agents according to the
invention, cancer is breast cancer, the P53 isoform which
expression is detected in step a) is .DELTA.133p53.beta. isoform or
.DELTA.133p53.beta. and .DELTA.133p53.gamma. isoforms, its/their
the expression level(s) is/are measured at the nucleic level by
measuring the amount of mRNA or corresponding cDNA (preferably by
q-RT-PCR), and sphere-forming ability is detected by the preferred
assay described in Table 9 above.
[0286] The following examples merely intend to illustrate the
present invention.
EXAMPLES
Example 1: Materials and Methods
[0287] The following is a description of materials and methods used
in following examples.
Plasmids
[0288] The human .DELTA.133p53 isoforms (.alpha., .beta. and
.gamma.) were cloned with (Sh1-resistant variants) or without 3'
fusion Flag tag in the pMSCVhyg (Clontech Laboratories) plasmid for
retroviral production. Site-directed mutagenesis to obtain
Sh1-resistant p53 isoforms was performed using the QuickChange II
(Stratagene) mutagenesis kit. The silent mutation was introduced
using the following oligonucleotide:
TABLE-US-00012 (SEQ ID NO: 17)
5'-CATCACACTGGAAGATTCTAGCGGCAATCTACTGGGACG-3'
(the underlined region is targeted by Sh1).
[0289] ShRNAs (Sh) were cloned in the RNAi-Ready pSIREN-Retro Q
plasmid (Clontech Laboratories). The Sh sequences used in this
study are (see also FIG. 1):
TABLE-US-00013 (SEQ ID NO: 13) Sh1: 5'-GACTCCAGTGGTAATCTAC-3' (SEQ
ID NO: 18) Sh2: 5'-GTCCAGATGAAGCTCCCAGAA-3' (SEQ ID NO: 14) Sh3:
5'-GGAGGTGCTTACACATGTT-3' (SEQ ID NO: 15) Sh4:
5'-CTTGTGCCCTGACTTTCAA-3' (SEQ ID NO: 16) Sh5:
5'-GGACCAGACCAGC1TTCA-3' (SEQ ID NO: 19) Sh6:
5'-GTGAGCGCTTCGAGATGTT-3'
[0290] All plasmids were verified by sequencing before use.
Cell Culture
[0291] The human breast cancer cell lines MCF-7, MDA-MB 231 D3H2LN
and C3LND were grown in MEM supplemented with 10% FCS, sodium
pyruvate and glutamine. Following viral infection, cells were used
after 24-48 h or subjected to selection with 2 .mu.g/ml puromycin
(InvivoGen) or 300 .mu.g/ml hygromycin B (Invitrogen) for two days.
Etoposide treatment was performed with final doses of 12.5, 25 and
50 ng/ml for 16 h or 50 ng/ml/day for 7 days.
[0292] For mammosphere formation, 1000 cells/ml (500 cells/well)
were plated in Ultra Low Cluster Plate, 24-well, Flat Bottom
(Corning Inc) with MammoCult.TM. Medium enriched with MammoCult.TM.
Proliferation Supplements, hydrocortisone and heparin (Stem Cell
Technologies) and cultured for 15 days. For all mammosphere assays,
at least three independent experiments for each condition were
carried out and repeated 8-12 times. For self-renewal experiments,
transfected cells were subjected to a first cycle of mammosphere
formation. Upon 15 days of culture the created mammospheres were
dissociated and cells were re-plated in identical conditions as for
the first plating.
[0293] The same protocol has been used with human colon carcinoma
cell line SW480.
MDA-MB231 C3LND Cell Line Establishment
[0294] The C3LND cell line was derived from distant metastases of
the MDA-MB231-luc-D3H2LN cell line after two in vivo passages in
nude mice.
[0295] Briefly, 1.times.10.sup.6 cells per animal were resuspended
in sterile PBS for intracardiac injections (first cycle of
enrichment) or in 50% Matrigel (BD Biosciences, USA) for injection
in the lower left mammary fat pad (second cycle of enrichment) of
athymic nude mice (Hsd:Athymic Nude-Foxn1, Harlan). Tumor
progression and time to metastasis were followed weekly by whole
body bioluminescence imaging. Invaded organs were then resected and
tumor cells isolated and propagated in vitro.
In Vivo Experiments
[0296] All in vivo experiments were performed in compliance with
the French regulations and ethical guidelines for experimental
animal studies in an accredited establishment (Agreement No.
C34-172-27). 2.10.sup.6 control or Sh3-treated C3LND cancer cells
were grafted in 6 week-old female athymic mice (Harlan, Le
Malourlet, France) by intracardiac injection (n=5-7/group).
Bioluminescence detection was used to monitor tumor growth and
distal metastasis formation in head and legs. Regions of interest
(ROI) were delineated around the tumor sites and the total flux
(ph/s) in the ROI was measured.
Antibodies, Immunoblotting and Immunofluorescence
[0297] The following antibodies were used for immunoblotting:
anti-c-Myc (9E10 mouse hybridoma clone), -Nanog (sc-81961, Santa
Cruz Biotechnology), -Oct 3/4 (sc-8630, Santa Cruz Biotechnology),
-Sox 2 (sc-17320, Santa Cruz Biotechnology), -p53 (D0-1; sc-126
Santa Cruz Biotechnology), -p53 Sapu (Vojtesek et al. 1995),
-.alpha.-tubulin (clone DM1A, Sigma-Aldrich), -.beta.-actin (clone
AC-74 Sigma-Aldrich), -p21 (sc-397 Santa Cruz Biotechnology) and
-Flag (clone M2; Sigma-Aldrich). Secondary HRP-conjugated
antibodies were from GE Healthcare. For luminescence
quantification, cells were serially diluted and incubated with 0.5
mM D-luciferin (Sigma). Luminescence was quantified with a
Polarstar Omega instrument (BMG LABTECH).
Flow Cytometry Analysis
[0298] Single cell suspensions were labeled on ice with CD24-FITC,
CD44-PE and their respective isotype controls (BioLegend) at the
dilutions indicated by the manufacturer in Phosphate Buffered
Saline (PBS) with 10% FBS for 30 min. Cells were then washed once
with PBS and re-suspended in PBS/10% FBS. All samples were analyzed
on a CyAn analyzer (Becton Coulter, Inc) using Sytox Blue (Life
Technologies) to monitor cell viability.
RNA Extraction and RT-qPCR
[0299] Total RNA was extracted (Qiagen) and reverse transcription
(RT) was performed with 1-5 .mu.g of total RNA using the
SuperScript.RTM. III Reverse Transcriptase (Life Technologies) at
50.degree. C. Levels of different mRNAs were quantified by
real-time qPCR on a LightCycler480 apparatus (Roche). Briefly, 20
ng cDNA was amplified using 0.168 .mu.M of each primer, 0.2 .mu.M
of probe (Table 4) and 1.times. LightCycler.RTM. 480 Probes Master
Mix (Roche) for the p53 isoforms, or commercially available primers
(Qiagen) and 1.times. LightCycler.RTM. 480 Sybr Green Master Mix
(Roche) for the other genes. Data were normalized to the internal
standard TBP. The different primers used and their corresponding
sequences have been previously described (Bourdon et al., 2005).
For each single-well amplification reaction, a threshold cycle (Ct)
was calculated by using the LightCycler480 program (Roche) in the
exponential phase of amplification. Relative changes in gene
expression were determined using the 2.DELTA..DELTA.Ct method and
reported relative to a control. All quantification studies were
performed with at least three independent experiments, repeated
twice, for each condition. Data are presented as the arithmetic
mean.+-.SEM.
Statistical Analysis
[0300] All data are presented as the arithmetic mean.+-.SEM.
Statistical analyses were performed using the non-parametric
Mann-Whitney t-test with the Prism software (GraphPad
Software).
Example 2: Changes in the Expression of p53 Isoforms Affect
Mammosphere Formation
[0301] To study the role of the different p53 isoforms in CSC
potential we designed shRNAs (Sh) that selectively silence specific
groups of isoforms (FIG. 1A). Briefly, Sh1 knocks down all p53
isoforms, while Sh2 targets the long TAp53 (trans-activating) and
.DELTA.40p53 isoforms. Sh3 and Sh4 target the 5' UTR of the
.DELTA.133 isoforms (.alpha., .beta. and .gamma.) and Sh5 and Sh6
respectively target the 3' end of the .beta. and .alpha.
isoforms.
[0302] First we tested the ability of MCF-7 cells to form
mammospheres, an assay widely used to assess CSC potential in
vitro. Silencing of all p53 isoforms (with Sh1) resulted in a
significant reduction of mammosphere formation compared to control
cells, while knock-down of the TAp53 and .DELTA.40p53 isoforms
(Sh2) had no effect (FIGS. 1B and C). In parallel we measured the
mRNA (FIG. 1F) and protein (FIG. 2A) expression of c-Myc, Sox 2,
Oct 3/4 and Nanog, which are key regulators of cell pluripotency.
TAp53 and .DELTA.40p53 (Sh2) silencing resulted in increased
expression of Oct 3/4, Nanog and Sox 2, but not of c-Myc, while
depletion of all p53 isoforms (Sh1) had no effect. Moreover,
depletion of TAp53 and .DELTA.40p53 (Sh2) increased the expression
of the .DELTA.133 isoforms (FIG. 1G).
[0303] These results suggest that CSC potential in MCF-7 cells is
not only regulated by TAp53.alpha., which was previously identified
as a suppressor of sternness. To investigate this hypothesis, we
depleted all .DELTA.133 isoforms using two different shRNAs (Sh3
and 4). Both shRNAs, used either alone or in combination,
significantly reduced mammosphere formation in MCF-7 cells,
suggesting that these isoforms are key regulators of CSC potential
(FIGS. 1B and D). Accordingly, Oct 3/4, Nanog and Sox 2, were
significantly down-regulated in .DELTA.133 isoform-silenced cells
(FIG. 2A). Again c-Myc expression was not affected. We then
evaluated the effect of .beta. and .alpha. isoform silencing.
Mammosphere formation was significantly reduced in cells in which
.beta. isoforms where knocked down (Sh5; FIG. 1A). Silencing of all
.alpha. isoforms (Sh6) did not affect mammosphere formation (Sh6;
FIGS. 2B and 2C). Altogether these findings suggest that
.DELTA.133p53 (.alpha., (.beta., .gamma.) isoforms are involved in
regulating CSC potential in MCF-7 cells.
[0304] The inventors also investigated the ability of
.DELTA.133p53.beta. isoform in promoting CSC potential in colon
carcinoma cells SW480. For that, as described above .DELTA.133p53
isoforms were knocked-down by using a shRNA (Sh3) in SW480 colon
carcinoma cells.
[0305] As demonstrated previously with MCF-7 breast cancer cell
line, the results obtained with colon carcinoma cell line SW480
(FIG. 2D) also suggest that silencing .DELTA.133p53.beta.
expression significantly reduced colospheres formation in these
cells compared to control shLuc, indicating that these isoforms are
key regulators of CSC potential in colon cancer also.
[0306] The same results may be expected with all cancers for which
it has been demonstrated that transcriptional factors Sox 2, Oct
3/4 and/or Nanog are involved in CSCs induction from cancer
cells.
Example 3: The .DELTA.133p53B Isoform Promotes Cancer Stem Cell
Potential in MCF-7 Cells
[0307] Indeed, mammosphere formation was significantly increased in
MCF-7 that express only the .DELTA.133p53.beta. and
.DELTA.133p53.gamma. isoforms following concomitant transduction
with Sh2 and Sh6 (FIGS. 3A and 3B), suggesting an inhibitory effect
of the .DELTA.133p53.alpha. isoform. To confirm that sphere
increase is indicative of CSC phenotype, we analyzed the proportion
of CD44.sup.+/CD24.sup.- cells because this subpopulation of cancer
cells are considered to have CSC properties. Similarly to
mammosphere formation variations, the proportion of
CD44.sup.+/CD24.sup.- cells was not affected by TAp53 and
.DELTA.40p53 isoform silencing with Sh2, whereas it was increased
by co-transduction of Sh2 and Sh6 (FIG. 3C). To determine the
specific contribution of the .DELTA.133p53 (.beta. and .gamma.)
isoforms in promoting mammosphere formation, we overexpressed them
separately. In agreement with the previous results, over-expression
of .DELTA.133p53.beta. significantly promoted mammosphere
formation, while .gamma. isoform over-expression had a milder
effect (FIG. 3D and FIG. 4). Moreover, .DELTA.133p53.beta.
over-expression resulted in a significant increase of Sox 2, Nanog
and Oct 3/4 expression, but not of c-Myc (FIG. 3E). In addition,
mammosphere formed with .DELTA.133p53.beta. was higher after
harvesting and re-plating of primary mammospheres, considered as
the gold standard experiment to challenge CSC phenotype in vitro
(FIG. 3F).
[0308] Finally, to confirm the role of the .DELTA.133p53.beta.
isoform in promoting CSC potential in MCF-7 cells, we overexpressed
a Sh1-resistant .DELTA.133p53.beta. isoform in MCF-7 cells in which
all p53 isoforms had been knocked down with Sh1. As expected,
expression of Sh1-resistant .DELTA.133p53.beta. rescued mammosphere
formation (FIG. 3G).
[0309] Altogether these results indicate that the
.DELTA.133p53.beta. isoform positively regulates CSC potential in
MCF-7 breast cancer cells.
Example 4: High .DELTA.133p53 Levels Correlate with Increased
Metastatic Capacity and Mammosphere Formation Ability
[0310] Increasing evidences suggest that CSC phenotype and
metastasis development are closely linked. We therefore sought to
determine whether the metastatic capacity of breast cancer cells
was coupled to their CSC potential and .DELTA.133p53 isoform
expression. To this end, we used MDA-MB-231 D3H2LN cells, which can
generate at low frequency lung metastasis when transplanted in
immuno-deficient mice, to derive the highly cancer-prone and very
metastatic C3LND cell line (see Methods in Example 1) (FIG. 5A).
When this line was used for orthotopic transplantation experiments
in nude mice, metastasis detection time was reduced from 82 days
(with parental D3H2LN cells) to 20 days and lung metastases were
detected in all transplanted animals (FIG. 5B). Although primary
tumor growth was comparable in both cell lines (FIG. 5C),
metastasis development was significantly accelerated in C3LND cells
as indicated by bioluminescence quantification (FIG. 5D).
[0311] Evaluation of mammosphere formation in D3H2LN and C3LND
cells showed that these latter formed two-times more mammospheres
(FIG. 6A). Similarly, .DELTA.133p53 isoforms expression was 3-fold
higher and Oct 3/4, Nanog and Sox 2 levels were 2-3-fold higher in
C3LND (FIGS. 6B and C). c-Myc expression was comparable in the two
cells lines. We then asked whether pluripotency factor expression
could be affected by changes in .DELTA.133p53 expression.
Overexpression of .DELTA.133p53.beta. in D3H2LN cells resulted in a
significant increase of Oct 3/4, Nanog and Sox 2 expression,
whereas c-Myc level was not affected, consistent with data obtained
in MCF-7 cells (FIGS. 6D and 6E). Similar results were obtained in
C3LND cells (FIG. 5F). In complete agreement with observations in
MCF-7, .DELTA.133p53.beta. overexpression in D3H2LN cells resulted
in a significant increase of mammosphere formation (FIG. 6F).
[0312] Conversely, Sh3-mediated knock-down of the .DELTA.133p53
isoforms in C3LND cells led to a significant reduction of sphere
formation associated with a marked decrease of Oct 3/4, Nanog and
Sox 2 expression and a small increase of c-Myc level (FIGS. 6G, H
and I), whereas .DELTA.133p53.beta. transduction increased them
(FIG. 5F). In agreement, transduction of Sh3 decreased the
proportion of CD44.sup.+/CD24.sup.- cells (FIG. 6J) Finally, after
intracardiac injection in athymic mice, Sh3-transduced C3LND cells
were less prone to metastasize to distant sites compared to control
cells (FIG. 6K and FIG. 5G). In summary, the more metastatic C3LND
cell line is characterized by higher CSC potential, as indicated by
mammosphere formation, and increased .DELTA.133p53 as well as Oct
3/4, Nanog and Sox 2 (but not c-Myc) expression compared to the
parental D3H2LN cell line. .DELTA.133p53 overexpression increases
the pluripotency potential of D3H2LN cells, while its knock-down
produces the opposite effect and a marked reduction of the
metastatic potential of these cells when grafted in mice.
Altogether these data suggest that the .DELTA.133p53.beta. isoform
specifically regulates CSC activity and metastasis formation
through modulation of the expression of key players in the
maintenance of cell pluripotency and reprogramming (i.e., Oct 3/4,
Nanog and Sox 2).
Example 5: Chemotherapy Treatment of Breast Cancer Cell Lines
Up-Regulates the Expression of .DELTA.133p53 Isoforms and Activates
Key Reprogramming Genes
[0313] Topoisomerase II inhibitors (etoposide-VP16 and doxorubicin)
are frequently used as adjuvant chemotherapy treatment for several
cancer types alone or in combination with other drugs (cisplatin
most frequently). Topoisomerase II inhibitors induce double strand
DNA breaks, a genotoxic stress that strongly activates p53
signaling. Up-regulation of TAp53 should be beneficial due to its
ability to induce cell cycle arrest, apoptosis and to negatively
regulate cell reprogramming. We thus assessed whether etoposide
could affect .DELTA.133p53 expression and CSC potential in breast
cancer cell lines. Increasing concentrations of etoposide resulted
in TAp53.alpha. stabilization in MCF-7. As expected, p21 expression
(positively regulated by p53) was increased, whereas c-Myc
expression (negatively regulated by p53) was reduced (FIG. 7A), as
also confirmed by RT-qPCR quantification (FIG. 7B). Moreover,
RT-qPCR and western blot analysis showed that, upon etoposide
treatment, .DELTA.133p53 isoforms (FIGS. 7C and 7D) as well as Oct
3/4, Nanog and Sox 2 (FIG. 7E) were strongly up-regulated in a
dose-dependent manner. This last result is particularly intriguing
because TAp53.alpha., which is considered as a negative regulator
of pluripotency/reprogramming genes, is stabilized and
transcriptionally active.
[0314] To determine whether Oct 3/4, Nanog and Sox2 up-regulation
in this condition required .DELTA.133p53 expression, we transduced
MCF-7 cells with Sh3 to specifically knock them down. Oct 3/4,
Nanog and Sox2 expression was reduced in both treated and etoposide
untreated cells following .DELTA.133p53 silencing (FIG. 7F),
confirming the specific role of .DELTA.133p53 isoforms in the
regulation of genes involved in cell
pluripotency/reprogramming.
[0315] Finally, we evaluated the effect of etoposide treatment on
mammosphere formation of Sh2-transduced MCF-7 cells. Etoposide
treatment in control cells (active TAp53) significantly reduced
mammosphere formation, whereas it did not have any significant
effect in Sh2-transduced cells (FIG. 7G). Moreover, .DELTA.133p53
level was correlated with the expression of reprogramming genes
(FIGS. 7H and 7I). These data indicate that TAp53 and
.DELTA.133p53B have an antagonistic action in sphere formation.
[0316] We then evaluated the effects of etoposide treatment in
MDA-MB-231 D3H2LN cells. This cell line harbors the p53 R280K
mutation and corresponds to a triple negative breast cancer type.
This mutation is present in TAp53 and also in .DELTA.133p53
isoforms. Incubation with increasing concentrations of etoposide
did not affect TAp53 expression, and p21 expression was only weakly
increased (FIG. 8A). This effect of mutant p53 protein on p21
expression was already described in literature (Bieging et al.,
2014). Interestingly, c-Myc expression was significantly
down-regulated, (FIGS. 8A and 8B). The expression of .DELTA.133p53
isoforms was up-regulated (FIGS. 8A and 8C), but not in a
dose-dependent manner as observed in MCF-7 cells. Similarly, the
expression of Nanog, Sox 2 and Oct 3/4 (FIG. 8D) was also
up-regulated following incubation with etoposide, like for
.DELTA.133p53 isoforms.
[0317] All together these data suggest that, in human breast cancer
cells, the topoisomerase II inhibitor etoposide increases
.DELTA.133p53 expression, resulting in the activation of the
reprogramming genes Nanog, Sox 2 and Oct 3/4.
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Sequence CWU 1
1
191209PRTHomo sapiensSITE(1)..(209)Homo sapiens tumor protein p53,
isoform delta133p53beta (Genbank NP_001119588.1) 1Met Phe Cys Gln
Leu Ala Lys Thr Cys Pro Val Gln Leu Trp Val Asp1 5 10 15Ser Thr Pro
Pro Pro Gly Thr Arg Val Arg Ala Met Ala Ile Tyr Lys 20 25 30Gln Ser
Gln His Met Thr Glu Val Val Arg Arg Cys Pro His His Glu 35 40 45Arg
Cys Ser Asp Ser Asp Gly Leu Ala Pro Pro Gln His Leu Ile Arg 50 55
60Val Glu Gly Asn Leu Arg Val Glu Tyr Leu Asp Asp Arg Asn Thr Phe65
70 75 80Arg His Ser Val Val Val Pro Tyr Glu Pro Pro Glu Val Gly Ser
Asp 85 90 95Cys Thr Thr Ile His Tyr Asn Tyr Met Cys Asn Ser Ser Cys
Met Gly 100 105 110Gly Met Asn Arg Arg Pro Ile Leu Thr Ile Ile Thr
Leu Glu Asp Ser 115 120 125Ser Gly Asn Leu Leu Gly Arg Asn Ser Phe
Glu Val Arg Val Cys Ala 130 135 140Cys Pro Gly Arg Asp Arg Arg Thr
Glu Glu Glu Asn Leu Arg Lys Lys145 150 155 160Gly Glu Pro His His
Glu Leu Pro Pro Gly Ser Thr Lys Arg Ala Leu 165 170 175Pro Asn Asn
Thr Ser Ser Ser Pro Gln Pro Lys Lys Lys Pro Leu Asp 180 185 190Gly
Glu Tyr Phe Thr Leu Gln Asp Gln Thr Ser Phe Gln Lys Glu Asn 195 200
205Cys22404DNAHomo sapiensmisc_featureHomo sapiens tumor protein
p53, isoform delta133p53beta (Genbank NM_001126116.1) 2tgaggccagg
agatggaggc tgcagtgagc tgtgatcaca ccactgtgct ccagcctgag 60tgacagagca
agaccctatc tcaaaaaaaa aaaaaaaaaa gaaaagctcc tgaggtgtag
120acgccaactc tctctagctc gctagtgggt tgcaggaggt gcttacgcat
gtttgtttct 180ttgctgccgt cttccagttg ctttatctgt tcacttgtgc
cctgactttc aactctgtct 240ccttcctctt cctacagtac tcccctgccc
tcaacaagat gttttgccaa ctggccaaga 300cctgccctgt gcagctgtgg
gttgattcca cacccccgcc cggcacccgc gtccgcgcca 360tggccatcta
caagcagtca cagcacatga cggaggttgt gaggcgctgc ccccaccatg
420agcgctgctc agatagcgat ggtctggccc ctcctcagca tcttatccga
gtggaaggaa 480atttgcgtgt ggagtatttg gatgacagaa acacttttcg
acatagtgtg gtggtgccct 540atgagccgcc tgaggttggc tctgactgta
ccaccatcca ctacaactac atgtgtaaca 600gttcctgcat gggcggcatg
aaccggaggc ccatcctcac catcatcaca ctggaagact 660ccagtggtaa
tctactggga cggaacagct ttgaggtgcg tgtttgtgcc tgtcctggga
720gagaccggcg cacagaggaa gagaatctcc gcaagaaagg ggagcctcac
cacgagctgc 780ccccagggag cactaagcga gcactgccca acaacaccag
ctcctctccc cagccaaaga 840agaaaccact ggatggagaa tatttcaccc
ttcaggacca gaccagcttt caaaaagaaa 900attgttaaag agagcatgaa
aatggttcta tgactttgcc tgatacagat gctacttgac 960ttacgatggt
gttacttcct gataaactcg tcgtaagttg aaaatattat ccgtgggcgt
1020gagcgcttcg agatgttccg agagctgaat gaggccttgg aactcaagga
tgcccaggct 1080gggaaggagc caggggggag cagggctcac tccagccacc
tgaagtccaa aaagggtcag 1140tctacctccc gccataaaaa actcatgttc
aagacagaag ggcctgactc agactgacat 1200tctccacttc ttgttcccca
ctgacagcct cccaccccca tctctccctc ccctgccatt 1260ttgggttttg
ggtctttgaa cccttgcttg caataggtgt gcgtcagaag cacccaggac
1320ttccatttgc tttgtcccgg ggctccactg aacaagttgg cctgcactgg
tgttttgttg 1380tggggaggag gatggggagt aggacatacc agcttagatt
ttaaggtttt tactgtgagg 1440gatgtttggg agatgtaaga aatgttcttg
cagttaaggg ttagtttaca atcagccaca 1500ttctaggtag gggcccactt
caccgtacta accagggaag ctgtccctca ctgttgaatt 1560ttctctaact
tcaaggccca tatctgtgaa atgctggcat ttgcacctac ctcacagagt
1620gcattgtgag ggttaatgaa ataatgtaca tctggccttg aaaccacctt
ttattacatg 1680gggtctagaa cttgaccccc ttgagggtgc ttgttccctc
tccctgttgg tcggtgggtt 1740ggtagtttct acagttgggc agctggttag
gtagagggag ttgtcaagtc tctgctggcc 1800cagccaaacc ctgtctgaca
acctcttggt gaaccttagt acctaaaagg aaatctcacc 1860ccatcccaca
ccctggagga tttcatctct tgtatatgat gatctggatc caccaagact
1920tgttttatgc tcagggtcaa tttctttttt cttttttttt tttttttttc
tttttctttg 1980agactgggtc tcgctttgtt gcccaggctg gagtggagtg
gcgtgatctt ggcttactgc 2040agcctttgcc tccccggctc gagcagtcct
gcctcagcct ccggagtagc tgggaccaca 2100ggttcatgcc accatggcca
gccaactttt gcatgttttg tagagatggg gtctcacagt 2160gttgcccagg
ctggtctcaa actcctgggc tcaggcgatc cacctgtctc agcctcccag
2220agtgctggga ttacaattgt gagccaccac gtccagctgg aagggtcaac
atcttttaca 2280ttctgcaagc acatctgcat tttcacccca cccttcccct
ccttctccct ttttatatcc 2340catttttata tcgatctctt attttacaat
aaaactttgc tgccacctgt gtgtctgagg 2400ggtg 24043214PRTHomo
sapiensSITE(1)..(214)Homo sapiens tumor protein p53, isoform
delta133p53gamma (Genbank NP_001119589.1) 3Met Phe Cys Gln Leu Ala
Lys Thr Cys Pro Val Gln Leu Trp Val Asp1 5 10 15Ser Thr Pro Pro Pro
Gly Thr Arg Val Arg Ala Met Ala Ile Tyr Lys 20 25 30Gln Ser Gln His
Met Thr Glu Val Val Arg Arg Cys Pro His His Glu 35 40 45Arg Cys Ser
Asp Ser Asp Gly Leu Ala Pro Pro Gln His Leu Ile Arg 50 55 60Val Glu
Gly Asn Leu Arg Val Glu Tyr Leu Asp Asp Arg Asn Thr Phe65 70 75
80Arg His Ser Val Val Val Pro Tyr Glu Pro Pro Glu Val Gly Ser Asp
85 90 95Cys Thr Thr Ile His Tyr Asn Tyr Met Cys Asn Ser Ser Cys Met
Gly 100 105 110Gly Met Asn Arg Arg Pro Ile Leu Thr Ile Ile Thr Leu
Glu Asp Ser 115 120 125Ser Gly Asn Leu Leu Gly Arg Asn Ser Phe Glu
Val Arg Val Cys Ala 130 135 140Cys Pro Gly Arg Asp Arg Arg Thr Glu
Glu Glu Asn Leu Arg Lys Lys145 150 155 160Gly Glu Pro His His Glu
Leu Pro Pro Gly Ser Thr Lys Arg Ala Leu 165 170 175Pro Asn Asn Thr
Ser Ser Ser Pro Gln Pro Lys Lys Lys Pro Leu Asp 180 185 190Gly Glu
Tyr Phe Thr Leu Gln Met Leu Leu Asp Leu Arg Trp Cys Tyr 195 200
205Phe Leu Ile Asn Ser Ser 21042331DNAHomo sapiensmisc_featureHomo
sapiens tumor protein p53, isoform delta133p53gamma (Genbank
NM_001126117.1) 4tgaggccagg agatggaggc tgcagtgagc tgtgatcaca
ccactgtgct ccagcctgag 60tgacagagca agaccctatc tcaaaaaaaa aaaaaaaaaa
gaaaagctcc tgaggtgtag 120acgccaactc tctctagctc gctagtgggt
tgcaggaggt gcttacgcat gtttgtttct 180ttgctgccgt cttccagttg
ctttatctgt tcacttgtgc cctgactttc aactctgtct 240ccttcctctt
cctacagtac tcccctgccc tcaacaagat gttttgccaa ctggccaaga
300cctgccctgt gcagctgtgg gttgattcca cacccccgcc cggcacccgc
gtccgcgcca 360tggccatcta caagcagtca cagcacatga cggaggttgt
gaggcgctgc ccccaccatg 420agcgctgctc agatagcgat ggtctggccc
ctcctcagca tcttatccga gtggaaggaa 480atttgcgtgt ggagtatttg
gatgacagaa acacttttcg acatagtgtg gtggtgccct 540atgagccgcc
tgaggttggc tctgactgta ccaccatcca ctacaactac atgtgtaaca
600gttcctgcat gggcggcatg aaccggaggc ccatcctcac catcatcaca
ctggaagact 660ccagtggtaa tctactggga cggaacagct ttgaggtgcg
tgtttgtgcc tgtcctggga 720gagaccggcg cacagaggaa gagaatctcc
gcaagaaagg ggagcctcac cacgagctgc 780ccccagggag cactaagcga
gcactgccca acaacaccag ctcctctccc cagccaaaga 840agaaaccact
ggatggagaa tatttcaccc ttcagatgct acttgactta cgatggtgtt
900acttcctgat aaactcgtcg taagttgaaa atattatccg tgggcgtgag
cgcttcgaga 960tgttccgaga gctgaatgag gccttggaac tcaaggatgc
ccaggctggg aaggagccag 1020gggggagcag ggctcactcc agccacctga
agtccaaaaa gggtcagtct acctcccgcc 1080ataaaaaact catgttcaag
acagaagggc ctgactcaga ctgacattct ccacttcttg 1140ttccccactg
acagcctccc acccccatct ctccctcccc tgccattttg ggttttgggt
1200ctttgaaccc ttgcttgcaa taggtgtgcg tcagaagcac ccaggacttc
catttgcttt 1260gtcccggggc tccactgaac aagttggcct gcactggtgt
tttgttgtgg ggaggaggat 1320ggggagtagg acataccagc ttagatttta
aggtttttac tgtgagggat gtttgggaga 1380tgtaagaaat gttcttgcag
ttaagggtta gtttacaatc agccacattc taggtagggg 1440cccacttcac
cgtactaacc agggaagctg tccctcactg ttgaattttc tctaacttca
1500aggcccatat ctgtgaaatg ctggcatttg cacctacctc acagagtgca
ttgtgagggt 1560taatgaaata atgtacatct ggccttgaaa ccacctttta
ttacatgggg tctagaactt 1620gacccccttg agggtgcttg ttccctctcc
ctgttggtcg gtgggttggt agtttctaca 1680gttgggcagc tggttaggta
gagggagttg tcaagtctct gctggcccag ccaaaccctg 1740tctgacaacc
tcttggtgaa ccttagtacc taaaaggaaa tctcacccca tcccacaccc
1800tggaggattt catctcttgt atatgatgat ctggatccac caagacttgt
tttatgctca 1860gggtcaattt cttttttctt tttttttttt ttttttcttt
ttctttgaga ctgggtctcg 1920ctttgttgcc caggctggag tggagtggcg
tgatcttggc ttactgcagc ctttgcctcc 1980ccggctcgag cagtcctgcc
tcagcctccg gagtagctgg gaccacaggt tcatgccacc 2040atggccagcc
aacttttgca tgttttgtag agatggggtc tcacagtgtt gcccaggctg
2100gtctcaaact cctgggctca ggcgatccac ctgtctcagc ctcccagagt
gctgggatta 2160caattgtgag ccaccacgtc cagctggaag ggtcaacatc
ttttacattc tgcaagcaca 2220tctgcatttt caccccaccc ttcccctcct
tctccctttt tatatcccat ttttatatcg 2280atctcttatt ttacaataaa
actttgctgc cacctgtgtg tctgaggggt g 23315393PRTHomo
sapiensSITE(1)..(393)Homo sapiens tumor protein p53 (Genbank
NP_000537.3) 5Met Glu Glu Pro Gln Ser Asp Pro Ser Val Glu Pro Pro
Leu Ser Gln1 5 10 15Glu Thr Phe Ser Asp Leu Trp Lys Leu Leu Pro Glu
Asn Asn Val Leu 20 25 30Ser Pro Leu Pro Ser Gln Ala Met Asp Asp Leu
Met Leu Ser Pro Asp 35 40 45Asp Ile Glu Gln Trp Phe Thr Glu Asp Pro
Gly Pro Asp Glu Ala Pro 50 55 60Arg Met Pro Glu Ala Ala Pro Pro Val
Ala Pro Ala Pro Ala Ala Pro65 70 75 80Thr Pro Ala Ala Pro Ala Pro
Ala Pro Ser Trp Pro Leu Ser Ser Ser 85 90 95Val Pro Ser Gln Lys Thr
Tyr Gln Gly Ser Tyr Gly Phe Arg Leu Gly 100 105 110Phe Leu His Ser
Gly Thr Ala Lys Ser Val Thr Cys Thr Tyr Ser Pro 115 120 125Ala Leu
Asn Lys Met Phe Cys Gln Leu Ala Lys Thr Cys Pro Val Gln 130 135
140Leu Trp Val Asp Ser Thr Pro Pro Pro Gly Thr Arg Val Arg Ala
Met145 150 155 160Ala Ile Tyr Lys Gln Ser Gln His Met Thr Glu Val
Val Arg Arg Cys 165 170 175Pro His His Glu Arg Cys Ser Asp Ser Asp
Gly Leu Ala Pro Pro Gln 180 185 190His Leu Ile Arg Val Glu Gly Asn
Leu Arg Val Glu Tyr Leu Asp Asp 195 200 205Arg Asn Thr Phe Arg His
Ser Val Val Val Pro Tyr Glu Pro Pro Glu 210 215 220Val Gly Ser Asp
Cys Thr Thr Ile His Tyr Asn Tyr Met Cys Asn Ser225 230 235 240Ser
Cys Met Gly Gly Met Asn Arg Arg Pro Ile Leu Thr Ile Ile Thr 245 250
255Leu Glu Asp Ser Ser Gly Asn Leu Leu Gly Arg Asn Ser Phe Glu Val
260 265 270Arg Val Cys Ala Cys Pro Gly Arg Asp Arg Arg Thr Glu Glu
Glu Asn 275 280 285Leu Arg Lys Lys Gly Glu Pro His His Glu Leu Pro
Pro Gly Ser Thr 290 295 300Lys Arg Ala Leu Pro Asn Asn Thr Ser Ser
Ser Pro Gln Pro Lys Lys305 310 315 320Lys Pro Leu Asp Gly Glu Tyr
Phe Thr Leu Gln Ile Arg Gly Arg Glu 325 330 335Arg Phe Glu Met Phe
Arg Glu Leu Asn Glu Ala Leu Glu Leu Lys Asp 340 345 350Ala Gln Ala
Gly Lys Glu Pro Gly Gly Ser Arg Ala His Ser Ser His 355 360 365Leu
Lys Ser Lys Lys Gly Gln Ser Thr Ser Arg His Lys Lys Leu Met 370 375
380Phe Lys Thr Glu Gly Pro Asp Ser Asp385 39062586DNAHomo
sapiensmisc_featureHomo sapiens tumor protein p53 cDNA (Genbank
NM_000546.4) 6gattggggtt ttcccctccc atgtgctcaa gactggcgct
aaaagttttg agcttctcaa 60aagtctagag ccaccgtcca gggagcaggt agctgctggg
ctccggggac actttgcgtt 120cgggctggga gcgtgctttc cacgacggtg
acacgcttcc ctggattggc agccagactg 180ccttccgggt cactgccatg
gaggagccgc agtcagatcc tagcgtcgag ccccctctga 240gtcaggaaac
attttcagac ctatggaaac tacttcctga aaacaacgtt ctgtccccct
300tgccgtccca agcaatggat gatttgatgc tgtccccgga cgatattgaa
caatggttca 360ctgaagaccc aggtccagat gaagctccca gaatgccaga
ggctgctccc cccgtggccc 420ctgcaccagc agctcctaca ccggcggccc
ctgcaccagc cccctcctgg cccctgtcat 480cttctgtccc ttcccagaaa
acctaccagg gcagctacgg tttccgtctg ggcttcttgc 540attctgggac
agccaagtct gtgacttgca cgtactcccc tgccctcaac aagatgtttt
600gccaactggc caagacctgc cctgtgcagc tgtgggttga ttccacaccc
ccgcccggca 660cccgcgtccg cgccatggcc atctacaagc agtcacagca
catgacggag gttgtgaggc 720gctgccccca ccatgagcgc tgctcagata
gcgatggtct ggcccctcct cagcatctta 780tccgagtgga aggaaatttg
cgtgtggagt atttggatga cagaaacact tttcgacata 840gtgtggtggt
gccctatgag ccgcctgagg ttggctctga ctgtaccacc atccactaca
900actacatgtg taacagttcc tgcatgggcg gcatgaaccg gaggcccatc
ctcaccatca 960tcacactgga agactccagt ggtaatctac tgggacggaa
cagctttgag gtgcgtgttt 1020gtgcctgtcc tgggagagac cggcgcacag
aggaagagaa tctccgcaag aaaggggagc 1080ctcaccacga gctgccccca
gggagcacta agcgagcact gcccaacaac accagctcct 1140ctccccagcc
aaagaagaaa ccactggatg gagaatattt cacccttcag atccgtgggc
1200gtgagcgctt cgagatgttc cgagagctga atgaggcctt ggaactcaag
gatgcccagg 1260ctgggaagga gccagggggg agcagggctc actccagcca
cctgaagtcc aaaaagggtc 1320agtctacctc ccgccataaa aaactcatgt
tcaagacaga agggcctgac tcagactgac 1380attctccact tcttgttccc
cactgacagc ctcccacccc catctctccc tcccctgcca 1440ttttgggttt
tgggtctttg aacccttgct tgcaataggt gtgcgtcaga agcacccagg
1500acttccattt gctttgtccc ggggctccac tgaacaagtt ggcctgcact
ggtgttttgt 1560tgtggggagg aggatgggga gtaggacata ccagcttaga
ttttaaggtt tttactgtga 1620gggatgtttg ggagatgtaa gaaatgttct
tgcagttaag ggttagttta caatcagcca 1680cattctaggt aggggcccac
ttcaccgtac taaccaggga agctgtccct cactgttgaa 1740ttttctctaa
cttcaaggcc catatctgtg aaatgctggc atttgcacct acctcacaga
1800gtgcattgtg agggttaatg aaataatgta catctggcct tgaaaccacc
ttttattaca 1860tggggtctag aacttgaccc ccttgagggt gcttgttccc
tctccctgtt ggtcggtggg 1920ttggtagttt ctacagttgg gcagctggtt
aggtagaggg agttgtcaag tctctgctgg 1980cccagccaaa ccctgtctga
caacctcttg gtgaacctta gtacctaaaa ggaaatctca 2040ccccatccca
caccctggag gatttcatct cttgtatatg atgatctgga tccaccaaga
2100cttgttttat gctcagggtc aatttctttt ttcttttttt tttttttttt
tctttttctt 2160tgagactggg tctcgctttg ttgcccaggc tggagtggag
tggcgtgatc ttggcttact 2220gcagcctttg cctccccggc tcgagcagtc
ctgcctcagc ctccggagta gctgggacca 2280caggttcatg ccaccatggc
cagccaactt ttgcatgttt tgtagagatg gggtctcaca 2340gtgttgccca
ggctggtctc aaactcctgg gctcaggcga tccacctgtc tcagcctccc
2400agagtgctgg gattacaatt gtgagccacc acgtccagct ggaagggtca
acatctttta 2460cattctgcaa gcacatctgc attttcaccc cacccttccc
ctccttctcc ctttttatat 2520cccattttta tatcgatctc ttattttaca
ataaaacttt gctgccacct gtgtgtctga 2580ggggtg 2586726DNAArtificial
sequenceForward primer for amplifying human delta133p53 isoforms
(Alpha, Beta and gamma) 7actctgtctc cttcctcttc ctacag
26821DNAArtificial sequenceReward primer for amplifying human
delta133p53 isoforms (Alpha, Beta and gamma) 8gtgtggaatc aacccacagc
t 21928DNAArtificial sequenceProbe for detecting human delta133p53
isoforms (Alpha, Beta and gamma) 9tcccctgccc tcaacaagat gttttgcc
281025DNAArtificial sequenceForward primer for amplifying human p53
beta isoforms (p53 TAbeta, delta40p53beta, delta133p53beta, and
delta160p53beta) 10aaccactgga tggagaatat ttcac 251126DNAArtificial
sequenceReward primer for amplifying human p53 beta isoforms (p53
TAbeta, delta40p53beta, delta133p53beta, and delta160p53beta)
11tcatagaacc attttcatgc tctctt 261234DNAArtificial sequenceProbe
for detecting human p53 beta isoforms (p53 TAbeta, delta40p53beta,
delta133p53beta, and delta160p53beta) 12caggaccaga ccagctttca
aaaagaaaat tgtt 341319DNAArtificial sequenceSequence of DBD domain
in all human p53 isoforms targeted by shRNA Sh1 13gactccagtg
gtaatctac 191419DNAArtificial sequenceSequence of 5? UTR of all
delta133 isoforms (Alpha, Beta and gamma) targeted by shRNA Sh3
14ggaggtgctt acacatgtt 191519DNAArtificial sequenceSequence of 5?
UTR of all delta133 isoforms (Alpha, Beta and gamma) targeted by
shRNA Sh4 15cttgtgccct gactttcaa 191618DNAArtificial
sequenceSequence of 3?end of all p53 beta isoforms (p53 TAbeta,
delta40p53beta, delta133p53beta, and delta160p53beta) targeted by
shRNA Sh5 16ggaccagacc agctttca 181739DNAArtificial
sequenceOligonucleotide for introducing resistance to Sh1
17catcacactg gaagattcta gcggcaatct actgggacg 391821DNAArtificial
sequenceSequence of TAD domain present in long TAp53 and delta40p53
isoforms targeted by shRNA Sh2 18gtccagatga agctcccaga a
211919DNAArtificial sequenceSequence of 3?end of all p53 alpha
isoforms (p53 TAalpha, delta40p53alpha, delta133p53alpha, and
delta160p53alpha) targeted by shRNA Sh6 19gtgagcgctt cgagatgtt
19
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